definition
expand assertion to
term replaced by
Class: ?X DisjointWith: RO_0002162 some ?Y
RO:0002161
external
never_in_taxon
true
true
never_in_taxon
never_in_taxon
Term not to be used for direct annotation
Term not to be used for direct manual annotation
AGR slim
Aspergillus GO slim
Candida GO slim
ChEMBL protein targets summary
FlyBase Drosophila GO ribbon slim
Generic GO slim
Metagenomics GO slim
Mouse GO slim
PIR GO slim
Plant GO slim
Fission yeast GO slim
synapse GO slim
Yeast GO slim
label approved by the SynGO project
Systematic synonym
subset_property
synonym_type_property
consider
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
has_scope
has_synonym_type
in_subset
shorthand
BFO:0000050
external
part_of
part_of
part of
BFO:0000051
external
has_part
has_part
has part
BFO:0000066
external
occurs_in
occurs_in
occurs in
RO:0002091
external
starts_during
starts_during
starts_during
RO:0002092
external
happens_during
happens_during
happens during
RO:0002093
external
ends_during
ends_during
ends_during
RO:0002211
external
regulates
regulates
regulates
RO:0002212
external
negatively_regulates
negatively_regulates
negatively regulates
RO:0002213
external
positively_regulates
positively_regulates
positively regulates
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
GO:0019952
GO:0050876
Wikipedia:Reproduction
reproductive physiological process
biological_process
GO:0000003
reproduction
The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
GOC:go_curators
GOC:isa_complete
GOC:jl
ISBN:0198506732
A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
nuclear interphase chromosome
cellular_component
GO:0000228
nuclear chromosome
A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
GOC:dph
GOC:mah
A chromosome found in the cytoplasm.
cytoplasmic interphase chromosome
cellular_component
GO:0000229
cytoplasmic chromosome
A chromosome found in the cytoplasm.
GOC:mah
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
GO:0007067
MIPS_funcat:10.03.01
MIPS_funcat:10.03.01.01
Wikipedia:Mitosis
biological_process
mitosis
GO:0000278
mitotic cell cycle
Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
GOC:mah
ISBN:0815316194
Reactome:69278
The developmental process in which the size or shape of a cell is generated and organized.
GO:0007148
GO:0045790
GO:0045791
MIPS_funcat:40.01
cellular morphogenesis
biological_process
GO:0000902
cell morphogenesis
The developmental process in which the size or shape of a cell is generated and organized.
GOC:clt
GOC:dph
GOC:go_curators
GOC:tb
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
Wikipedia:Immune_system
biological_process
GO:0002376
Note that this term is a direct child of 'biological_process ; GO:0008150' because some immune system processes are types of cellular process (GO:0009987), whereas others are types of multicellular organism process (GO:0032501). This term was added by GO_REF:0000022.
immune system process
Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
GOC:add
GOC:mtg_15nov05
GO_REF:0000022
A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism.
Wikipedia:Circulatory_system
biological_process
GO:0003013
circulatory system process
A organ system process carried out by any of the organs or tissues of the circulatory system. The circulatory system is an organ system that moves extracellular fluids to and from tissue within a multicellular organism.
GOC:mtg_cardio
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
GO:0005554
molecular function
molecular_function
GO:0003674
Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex.
molecular_function
A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process.
GOC:pdt
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0043566
MIPS_funcat:16.03.01
plasmid binding
molecular_function
microtubule/chromatin interaction
structure specific DNA binding
structure-specific DNA binding
GO:0003677
DNA binding
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GOC:dph
GOC:jl
GOC:tb
GOC:vw
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
kchris
2010-10-21T04:37:54Z
GO:0000130
GO:0001071
GO:0001130
GO:0001131
GO:0001151
GO:0001199
GO:0001204
nucleic acid binding transcription factor activity
transcription factor activity
DNA binding transcription factor activity
gene-specific transcription factor activity
sequence-specific DNA binding transcription factor activity
bacterial-type DNA binding transcription factor activity
bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding transcription factor activity
bacterial-type RNA polymerase transcription enhancer sequence-specific DNA binding transcription factor activity
bacterial-type RNA polymerase transcription factor activity, metal ion regulated sequence-specific DNA binding
bacterial-type RNA polymerase transcription factor activity, sequence-specific DNA binding
metal ion regulated sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity
metal ion regulated sequence-specific DNA binding transcription factor activity
sequence-specific DNA binding bacterial-type RNA polymerase transcription factor activity
transcription factor activity, bacterial-type RNA polymerase core promoter proximal region sequence-specific binding
transcription factor activity, bacterial-type RNA polymerase proximal promoter sequence-specific DNA binding
transcription factor activity, bacterial-type RNA polymerase transcription enhancer sequence-specific binding
transcription factor activity, metal ion regulated sequence-specific DNA binding
molecular_function
GO:0003700
Curator guidance: Note that most DNA-binding transcription factors do not have enzymatic activity. The presence of specific domains known to be present in DNA-binding transcription factors (HOX, GATA etc) should be used to help decide whether a protein is a DNA binding transcription factor or a coregulator. If a protein has an enzymatic activity (for example, ubiquitin ligase, histone acetyl transferase) and no known DNA binding domain, consider annotating to GO:0003712 transcription coregulator activity. Special care should be taken with proteins containing Myb/SANT and ARID domains, since only a subset of proteins containing these domains are DNA-binding transcription factors for specific genes.
Changed definition see https://github.com/geneontology/go-ontology/issues/15704
Merged term see https://github.com/geneontology/go-ontology/issues/16534
DNA-binding transcription factor activity
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
GOC:txnOH-2018
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
GO:0000498
GO:0044822
MIPS_funcat:16.03.03
Reactome:R-HSA-203922
base pairing with RNA
molecular_function
poly(A) RNA binding
poly(A)-RNA binding
poly-A RNA binding
GO:0003723
RNA binding
Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
GOC:jl
GOC:mah
Reactome:R-HSA-203922
Exportin-5 recognizes 3' overhang of pre-miRNA
Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
GO:0000499
base pairing with mRNA
molecular_function
GO:0003729
mRNA binding
Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
GOC:kmv
GOC:pr
SO:0000234
The action of a molecule that contributes to the structural integrity of the ribosome.
GO:0003736
GO:0003737
GO:0003738
GO:0003739
GO:0003740
GO:0003741
GO:0003742
ribosomal protein
molecular_function
ribosomal RNA
GO:0003735
Note that this term may be used to annotate ribosomal RNAs as well as ribosomal proteins.
structural constituent of ribosome
The action of a molecule that contributes to the structural integrity of the ribosome.
GOC:mah
Catalysis of the reaction: GTP + H2O = GDP + phosphate.
hydrolase activity, acting on acid anhydrides, acting on GTP, involved in cellular and subcellular movement
RHEA:19669
Reactome:R-HSA-1445143
Reactome:R-HSA-1458485
Reactome:R-HSA-156923
Reactome:R-HSA-164381
Reactome:R-HSA-165055
Reactome:R-HSA-167415
Reactome:R-HSA-170666
Reactome:R-HSA-170685
Reactome:R-HSA-170686
Reactome:R-HSA-177501
Reactome:R-HSA-203973
Reactome:R-HSA-2130641
Reactome:R-HSA-2130725
Reactome:R-HSA-2584246
Reactome:R-HSA-380979
Reactome:R-HSA-392133
Reactome:R-HSA-392212
Reactome:R-HSA-418574
Reactome:R-HSA-418582
Reactome:R-HSA-421835
Reactome:R-HSA-428941
Reactome:R-HSA-432707
Reactome:R-HSA-5333615
Reactome:R-HSA-5389839
Reactome:R-HSA-5389842
Reactome:R-HSA-5419273
Reactome:R-HSA-5419279
Reactome:R-HSA-555065
Reactome:R-HSA-5623513
Reactome:R-HSA-5638006
Reactome:R-HSA-5658231
Reactome:R-HSA-5665809
Reactome:R-HSA-5672017
Reactome:R-HSA-5694527
Reactome:R-HSA-6807877
Reactome:R-HSA-6814833
Reactome:R-HSA-8847534
Reactome:R-HSA-8847883
Reactome:R-HSA-8849082
Reactome:R-HSA-8854173
Reactome:R-HSA-8854255
Reactome:R-HSA-8854329
Reactome:R-HSA-8854604
Reactome:R-HSA-8854612
Reactome:R-HSA-8868661
Reactome:R-HSA-8981353
Reactome:R-HSA-8982020
Reactome:R-HSA-8982021
Reactome:R-HSA-8982025
Reactome:R-HSA-983422
ARF small monomeric GTPase activity
RHEB small monomeric GTPase activity
Rab small monomeric GTPase activity
Ran small monomeric GTPase activity
Ras small monomeric GTPase activity
Rho small monomeric GTPase activity
Sar small monomeric GTPase activity
dynamin GTPase activity
heterotrimeric G-protein GTPase activity
protein-synthesizing GTPase activity
protein-synthesizing GTPase activity, elongation
protein-synthesizing GTPase activity, initiation
protein-synthesizing GTPase activity, termination
signal-recognition-particle GTPase activity
small monomeric GTPase activity
tubulin GTPase activity
molecular_function
heterotrimeric G-protein GTPase, alpha-subunit
heterotrimeric G-protein GTPase, beta-subunit
heterotrimeric G-protein GTPase, gamma-subunit
GO:0003924
GTPase activity
Catalysis of the reaction: GTP + H2O = GDP + phosphate.
ISBN:0198547684
Reactome:R-HSA-1445143
RAB8A,10,13,14 hydrolyze GTP
Reactome:R-HSA-1458485
RALA hydrolyzes GTP
Reactome:R-HSA-156923
Hydrolysis of eEF1A:GTP
Reactome:R-HSA-164381
G alpha (s) auto-inactivates by hydrolysing GTP to GDP
Reactome:R-HSA-165055
Hydrolysis of Ran:GTP to Ran:GDP
Reactome:R-HSA-167415
G-protein alpha subunit is inactivated
Reactome:R-HSA-170666
Adenylate cyclase increases the GTPase activity of G alpha-olf
Reactome:R-HSA-170685
Adenylaye cyclase increases the GTPase activity of G alpha-olf
Reactome:R-HSA-170686
Adenylate cyclase increases the GTPase activity of Gi alpha
Reactome:R-HSA-177501
Endocytosis (internalization) of clathrin-coated vesicle
Reactome:R-HSA-203973
Vesicle budding
Reactome:R-HSA-2130641
Translocation of TGN-lysosome vesicle to lysosome
Reactome:R-HSA-2130725
Internalization of MHC II:Ii clathrin coated vesicle
Reactome:R-HSA-2584246
GNAT1-GTP hydrolyses its bound GTP to GDP
Reactome:R-HSA-380979
RHEB in mTORC1:RHEB:GTP hydrolyses GTP
Reactome:R-HSA-392133
G alpha (z) auto-inactivates by hydrolysing GTP to GDP
Reactome:R-HSA-392212
G alpha (i) auto-inactivates by hydrolysing GTP to GDP
Reactome:R-HSA-418574
G alpha (12/13) auto-inactivates by hydrolysing GTP to GDP
Reactome:R-HSA-418582
G alpha (q) auto-inactivates by hydrolysing GTP to GDP
Reactome:R-HSA-421835
trans-Golgi Network Vesicle Scission
Reactome:R-HSA-428941
P2Y purinoceptor 1 activates MAP kinase p38 alpha
Reactome:R-HSA-432707
trans-Golgi Network Lysosomal Vesicle Scission
Reactome:R-HSA-5333615
80S:Met-tRNAi:mRNA:SECISBP2:Sec-tRNA(Sec):EEFSEC:GTP is hydrolysed to 80S:Met-tRNAi:mRNA:SECISBP2:Sec and EEFSEC:GDP by EEFSEC
Reactome:R-HSA-5389839
39S subunit binds 28S subunit:mRNA:fMet-tRNA
Reactome:R-HSA-5389842
TUFM hydrolyzes GTP and TUFM:GDP dissociates from 55S ribosome
Reactome:R-HSA-5419273
Hydrolysis of GTP and dissociation of 28S and 39S subunits
Reactome:R-HSA-5419279
Translocation of peptidyl-tRNA from A-site to P-site (and translocation of 55S ribosome by 3 bases along mRNA)
Reactome:R-HSA-555065
Formation of clathrin coated vesicle
Reactome:R-HSA-5623513
ASAP1 stimulates GTPase activity of ARF4
Reactome:R-HSA-5638006
ARL3 hydrolyzes GTP
Reactome:R-HSA-5658231
RAS GAPs stimulate RAS GTPase activity
Reactome:R-HSA-5665809
SRGAP2 stimulates RAC1 GTP-ase activity and ends FMNL1-mediated elongation of actin filaments
Reactome:R-HSA-5672017
Rheb in the mTORC1 complex hydrolyses GTP
Reactome:R-HSA-5694527
Loss of SAR1B GTPase
Reactome:R-HSA-6807877
ARFGAPs stimulate ARF GTPase activity
Reactome:R-HSA-6814833
TBC1D20 stimulates GTPase activity of RAB1, resulting in hydrolysis of GTP
Reactome:R-HSA-8847534
RAB43 hydrolyses GTP
Reactome:R-HSA-8847883
CYTH proteins stimulate ARF1 GTPase activity
Reactome:R-HSA-8849082
ARHGAP35 stimulates RHOA GTPase activity
Reactome:R-HSA-8854173
TBC RabGAPs accelerate GTP hydrolysis by RAB35
Reactome:R-HSA-8854255
TBC1D2A accelerates GTP hydrolysis by RAB7
Reactome:R-HSA-8854329
TBC1D15 accelerates GTP hydrolysis by RAB7
Reactome:R-HSA-8854604
TBC1D16 accelerates GTP hydrolysis by RAB4A
Reactome:R-HSA-8854612
TBC1D25 accelerates GTP hydrolysis by RAB33B
Reactome:R-HSA-8868661
Dynamin-mediated GTP hydrolysis promotes vesicle scission
Reactome:R-HSA-8981353
RASA1 stimulates RAS GTPase activity
Reactome:R-HSA-8982020
G alpha (i)i1/i2/i3 in G (i):RGS complex is inactivated
Reactome:R-HSA-8982021
G alpha (z) in G alpha (z):RGS complex is inactivated
Reactome:R-HSA-8982025
G alpha (q) in G (q):RGS complex is inactivated
Reactome:R-HSA-983422
Disassembly of COPII coated vesicle
Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
GO:0008026
Reactome:R-HSA-167097
Reactome:R-HSA-169461
Reactome:R-HSA-169468
Reactome:R-HSA-5690996
Reactome:R-HSA-75949
Reactome:R-HSA-9613490
Reactome:R-HSA-9613494
Reactome:R-HSA-9613497
Reactome:R-HSA-9613498
ATP-dependent helicase activity
molecular_function
GO:0004386
Note that most helicases catalyze processive duplex unwinding.
helicase activity
Reactome:R-HSA-9613497
Unwinding DNA for the nascent transcript
Reactome:R-HSA-9613498
Unwinding of DNA for the nascent HIV-1 transcript
Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the unwinding of a DNA or RNA helix.
GOC:jl
Reactome:R-HSA-167097
HIV Promoter Opening: First Transition
Reactome:R-HSA-169461
MCM8 mediated fork unwinding
Reactome:R-HSA-169468
MCM2-7 mediated fork unwinding
Reactome:R-HSA-5690996
ERCC2 and ERCC3 DNA helicases form an open bubble structure in damaged DNA
Reactome:R-HSA-75949
RNA Polymerase II Promoter Opening: First Transition
Reactome:R-HSA-9613490
Unwinding of DNA for the nascent HIV-1 transcript: Second Transition
Reactome:R-HSA-9613494
Unwinding of DNA for the Nascent Transcript: Second Transition
Catalysis of the hydrolysis of ester linkages within nucleic acids.
EC:3.1
molecular_function
GO:0004518
Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', and 'DNA-(apurinic or apyrimidinic site) lyase activity ; GO:0003906' do not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis.
nuclease activity
Catalysis of the hydrolysis of ester linkages within nucleic acids.
ISBN:0198547684
The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
MIPS_funcat:16.07
molecular_function
GO:0005198
structural molecule activity
The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
GOC:mah
GOC:vw
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
GO:0008372
NIF_Subcellular:sao-1337158144
NIF_Subcellular:sao1337158144
cell or subcellular entity
cellular component
cellular_component
subcellular entity
GO:0005575
Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.
cellular_component
A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome).
GOC:pdt
NIF_Subcellular:sao-1337158144
subcellular entity
NIF_Subcellular:nlx_subcell_100315
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
MIPS_funcat:70.27
Wikipedia:Extracellular
extracellular
cellular_component
GO:0005576
Note that this term is intended to annotate gene products that are not attached to the cell surface. For gene products from multicellular organisms which are secreted from a cell but retained within the organism (i.e. released into the interstitial fluid or blood), consider the cellular component term 'extracellular space ; GO:0005615'.
extracellular region
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
GOC:go_curators
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
NIF_Subcellular:sao1425028079
cellular_component
intercellular space
GO:0005615
Note that for multicellular organisms, the extracellular space refers to everything outside a cell, but still within the organism (excluding the extracellular matrix). Gene products from a multi-cellular organism that are secreted from a cell into the interstitial fluid or blood can therefore be annotated to this term.
extracellular space
That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
ISBN:0198547684
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
MIPS_funcat:42.27.03
MIPS_funcat:70.01
Wikipedia:Cell_wall
cellular_component
GO:0005618
cell wall
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
GOC:giardia
ISBN:0198547684
PMID:15134259
http://en.wikipedia.org/wiki/Microbial_cyst
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
Wikipedia:Intracellular
internal to cell
protoplasm
cellular_component
nucleocytoplasm
protoplast
GO:0005622
intracellular
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
ISBN:0198506732
nucleocytoplasm
GOC:mah
protoplast
GOC:mah
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
cell and encapsulating structures
NIF_Subcellular:sao1813327414
Wikipedia:Cell_(biology)
cellular_component
GO:0005623
cell
The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
GOC:go_curators
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
MIPS_funcat:70.10
NIF_Subcellular:sao1702920020
Wikipedia:Cell_nucleus
cell nucleus
horsetail nucleus
cellular_component
GO:0005634
nucleus
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
GOC:go_curators
horsetail nucleus
GOC:al
GOC:mah
GOC:vw
PMID:15030757
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
GO:0005636
MIPS_funcat:70.10.05
Wikipedia:Nuclear_envelope
cellular_component
GO:0005635
nuclear envelope
The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
ISBN:0198547684
That part of the nuclear content other than the chromosomes or the nucleolus.
NIF_Subcellular:sao661522542
Wikipedia:Nucleoplasm
cellular_component
GO:0005654
nucleoplasm
That part of the nuclear content other than the chromosomes or the nucleolus.
GOC:ma
ISBN:0124325653
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
MIPS_funcat:70.10.03
Wikipedia:Chromosome
interphase chromosome
prophase chromosome
cellular_component
chromatid
GO:0005694
Chromosomes include parts that are not part of the chromatin. Examples include the kinetochore.
chromosome
A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
ISBN:0198547684
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
MIPS_funcat:70.10.07
NIF_Subcellular:sao1820400233
Wikipedia:Nucleolus
cellular_component
GO:0005730
nucleolus
A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
ISBN:0198506732
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
MIPS_funcat:70.03
Wikipedia:Cytoplasm
cellular_component
GO:0005737
cytoplasm
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
ISBN:0198547684
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
MIPS_funcat:70.16
NIF_Subcellular:sao1860313010
Wikipedia:Mitochondrion
mitochondria
cellular_component
GO:0005739
Some anaerobic or microaerophilic organisms (e.g. Entamoeba histolytica, Giardia intestinalis and several Microsporidia species) do not have mitochondria, and contain mitochondrion-related organelles (MROs) instead, called mitosomes or hydrogenosomes, very likely derived from mitochondria. To annotate gene products located in these mitochondrial relics in species such as Entamoeba histolytica, Giardia intestinalis or others, please use GO:0032047 'mitosome' or GO:0042566 'hydrogenosome'. (See PMID:24316280 for a list of species currently known to contain mitochondrion-related organelles.)
mitochondrion
A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
GOC:giardia
ISBN:0198506732
A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
MIPS_funcat:70.25
NIF_Subcellular:sao585356902
Wikipedia:Lysosome
cellular_component
GO:0005764
lysosome
A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
GOC:mah
ISBN:0198506732
A vacuole to which materials ingested by endocytosis are delivered.
MIPS_funcat:70.22
NIF_Subcellular:sao1720343330
Wikipedia:Endosome
cellular_component
GO:0005768
endosome
A vacuole to which materials ingested by endocytosis are delivered.
ISBN:0198506732
PMID:19696797
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
MIPS_funcat:70.25
Wikipedia:Vacuole
cellular_component
vacuolar carboxypeptidase Y
GO:0005773
vacuole
A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.
GOC:mtg_sensu
ISBN:0198506732
A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
GO:0019818
peroxisome vesicle
MIPS_funcat:70.19
NIF_Subcellular:sao499555322
Wikipedia:Peroxisome
cellular_component
peroxisomal
GO:0005777
peroxisome
A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.
GOC:pm
PMID:9302272
UniProtKB-KW:KW-0576
peroxisomal
GOC:curators
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
MIPS_funcat:70.07
NIF_Subcellular:sao1036339110
Wikipedia:Endoplasmic_reticulum
ER
cellular_component
GO:0005783
endoplasmic reticulum
The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
ISBN:0198506732
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
Golgi
MIPS_funcat:70.08
NIF_Subcellular:sao451912436
Wikipedia:Golgi_apparatus
Golgi complex
Golgi ribbon
cellular_component
GO:0005794
Note that the Golgi apparatus can be located in various places in the cytoplasm. In plants and lower animal cells, the Golgi apparatus exists as many copies of discrete stacks dispersed throughout the cytoplasm, while the Golgi apparatus of interphase mammalian cells is a juxtanuclear, often pericentriolar reticulum, where the discrete Golgi stacks are stitched together to form a compact and interconnected ribbon, sometimes called the Golgi ribbon.
Golgi apparatus
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
ISBN:0198506732
An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
adiposome
lipid body
lipid particle
cellular_component
GO:0005811
Note that this term does not refer to vesicles, but instead to structures in which lipids do not necessarily form bilayers.
lipid droplet
An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
GOC:mah
GOC:tb
An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
Wikipedia:Microtubule_organizing_center
MTOC
microtubule organising centre
cellular_component
GO:0005815
microtubule organizing center
An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
GOC:vw
ISBN:0815316194
PMID:17072892
PMID:17245416
http://en.wikipedia.org/wiki/Microtubule_organizing_center
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
NIF_Subcellular:sao101633890
Wikipedia:Cytosol
cellular_component
GO:0005829
cytosol
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GOC:hjd
GOC:jl
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
GO:0033279
NIF_Subcellular:sao1429207766
Wikipedia:Ribosome
free ribosome
membrane bound ribosome
cellular_component
ribosomal RNA
GO:0005840
ribosome
An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
ISBN:0198506732
free ribosome
NIF_Subcellular:sao1139385046
membrane bound ribosome
NIF_Subcellular:sao1291545653
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
MIPS_funcat:70.04
Wikipedia:Cytoskeleton
cellular_component
GO:0005856
cytoskeleton
Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
GOC:mah
ISBN:0198547684
PMID:16959967
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO:0005904
juxtamembrane
NIF_Subcellular:sao1663586795
Wikipedia:Cell_membrane
cell membrane
cellular membrane
cytoplasmic membrane
plasmalemma
bacterial inner membrane
inner endospore membrane
plasma membrane lipid bilayer
cellular_component
GO:0005886
plasma membrane
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
ISBN:0716731363
cellular membrane
NIF_Subcellular:sao6433132645
plasma membrane lipid bilayer
GOC:mah
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
GO:0072372
FMA:67181
NIF_Subcellular:sao787716553
Wikipedia:Cilium
eukaryotic flagellum
microtubule-based flagellum
primary cilium
cellular_component
flagellum
GO:0005929
Note that we deem cilium and microtubule-based flagellum to be equivalent. In most eukaryotic species, intracellular sub-components of the cilium, such as the ciliary base and rootlet, are located near the plasma membrane. In Diplomonads such as Giardia, instead, the same ciliary parts are located further intracellularly. Also, 'cilium' may be used when axonemal structure and/or motility are unknown, or when axonemal structure is unusual. For all other cases, please refer to children of 'cilium'. Finally, note that any role of ciliary proteins in sensory events should be captured by annotating to relevant biological process terms.
cilium
A specialized eukaryotic organelle that consists of a filiform extrusion of the cell surface and of some cytoplasmic parts. Each cilium is largely bounded by an extrusion of the cytoplasmic (plasma) membrane, and contains a regular longitudinal array of microtubules, anchored to a basal body.
GOC:cilia
GOC:curators
GOC:kmv
GOC:vw
ISBN:0198547684
PMID:16824949
PMID:17009929
PMID:20144998
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
janelomax
2012-10-23T15:40:34Z
GO:0044261
GO:0044723
MIPS_funcat:01.05
Wikipedia:Carbohydrate_metabolism
carbohydrate metabolism
multicellular organismal carbohydrate metabolic process
biological_process
single-organism carbohydrate metabolic process
GO:0005975
carbohydrate metabolic process
The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
GOC:mah
ISBN:0198506732
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
energy pathways
MIPS_funcat:02.45.15
biological_process
intermediary metabolism
metabolic energy generation
GO:0006091
generation of precursor metabolites and energy
The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
GOC:jl
intermediary metabolism
GOC:mah
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
GO:0055132
MIPS_funcat:10
MIPS_funcat:10.01
DNA metabolism
cellular DNA metabolism
biological_process
GO:0006259
DNA metabolic process
Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.
ISBN:0198506732
Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
MIPS_funcat:11.04.03
biological_process
mRNA maturation
GO:0006397
mRNA processing
Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
GOC:mah
The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established.
tRNA metabolism
biological_process
GO:0006399
tRNA metabolic process
The chemical reactions and pathways involving tRNA, transfer RNA, a class of relatively small RNA molecules responsible for mediating the insertion of amino acids into the sequence of nascent polypeptide chains during protein synthesis. Transfer RNA is characterized by the presence of many unusual minor bases, the function of which has not been completely established.
ISBN:0198506732
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
GO:0006416
GO:0006453
GO:0043037
MIPS_funcat:12
Wikipedia:Translation_(genetics)
protein anabolism
protein biosynthesis
protein biosynthetic process
protein formation
protein synthesis
protein translation
biological_process
GO:0006412
translation
The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
GOC:go_curators
protein biosynthetic process
GOC:curators
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
GO:0007022
GO:0007024
GO:0007025
MIPS_funcat:14
MIPS_funcat:14.01
Wikipedia:Protein_folding
alpha-tubulin folding
beta-tubulin folding
chaperonin-mediated tubulin folding
biological_process
chaperone activity
chaperonin ATPase activity
co-chaperone activity
co-chaperonin activity
glycoprotein-specific chaperone activity
non-chaperonin molecular chaperone ATPase activity
protein complex assembly, multichaperone pathway
GO:0006457
protein folding
The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
GOC:go_curators
GOC:rb
alpha-tubulin folding
GOC:mah
beta-tubulin folding
GOC:mah
chaperonin-mediated tubulin folding
GOC:mah
The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
protein modification process
MIPS_funcat:14
MIPS_funcat:14.07
MIPS_funcat:18.01.01
biological_process
process resulting in protein modification
protein tagging activity
GO:0006464
cellular protein modification process
The covalent alteration of one or more amino acids occurring in proteins, peptides and nascent polypeptides (co-translational, post-translational modifications) occurring at the level of an individual cell. Includes the modification of charged tRNAs that are destined to occur in a protein (pre-translation modification).
GOC:go_curators
protein modification process
GOC:bf
GOC:jl
The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
GO:0006519
MIPS_funcat:01.01
amino acid and derivative metabolism
amino acid metabolic process
cellular amino acid and derivative metabolic process
cellular amino acid metabolism
biological_process
GO:0006520
cellular amino acid metabolic process
The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.
CHEBI:33709
GOC:curators
ISBN:0198506732
amino acid and derivative metabolism
GOC:curators
amino acid metabolic process
GOC:curators
The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
MIPS_funcat:14
MIPS_funcat:14.04
Wikipedia:Protein_targeting
protein sorting along secretory pathway
biological_process
nascent polypeptide association
GO:0006605
Note that protein targeting encompasses the transport of the protein to the specified location, and may also include additional steps such as protein processing.
protein targeting
The process of targeting specific proteins to particular regions of the cell, typically membrane-bounded subcellular organelles. Usually requires an organelle specific protein sequence motif.
GOC:ma
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
MIPS_funcat:01.06
Wikipedia:Lipid_metabolism
lipid metabolism
biological_process
GO:0006629
lipid metabolic process
The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
GOC:ma
The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
MIPS_funcat:01.02
Wikipedia:Sulfur_metabolism
sulfur metabolism
sulphur metabolic process
sulphur metabolism
biological_process
GO:0006790
sulfur compound metabolic process
The chemical reactions and pathways involving the nonmetallic element sulfur or compounds that contain sulfur, such as the amino acids methionine and cysteine or the tripeptide glutathione.
GOC:ai
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
janelomax
2012-12-13T16:25:32Z
GO:0015457
GO:0015460
GO:0044765
MIPS_funcat:20
small molecule transport
solute:solute exchange
biological_process
single-organism transport
GO:0006810
Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport.
transport
The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
GOC:dos
GOC:dph
GOC:jl
GOC:mah
The directed movement of molecules between the nucleus and the cytoplasm.
GO:0000063
nucleocytoplasmic shuttling
biological_process
GO:0006913
Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane, and is not traversed.
nucleocytoplasmic transport
The directed movement of molecules between the nucleus and the cytoplasm.
GOC:go_curators
The cellular catabolic process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
GO:0016238
Wikipedia:Autophagy_(cellular)
biological_process
GO:0006914
autophagy
The cellular catabolic process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
GOC:autophagy
ISBN:0198547684
PMID:11099404
PMID:9412464
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
MIPS_funcat:32.01
biological_process
response to abiotic stress
response to biotic stress
GO:0006950
Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC.
response to stress
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
GOC:mah
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
MIPS_funcat:42.16
mitochondria organization
mitochondrion organisation
biological_process
mitochondrion organization and biogenesis
GO:0007005
mitochondrion organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrion; includes mitochondrial morphogenesis and distribution, and replication of the mitochondrial genome as well as synthesis of new mitochondrial components.
GOC:dph
GOC:jl
GOC:mah
GOC:sgd_curators
PMID:9786946
mitochondria organization
GOC:mah
mitochondrion organisation
GOC:mah
mitochondrion organization and biogenesis
GOC:curators
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.
MIPS_funcat:42.02
plasma membrane organisation
biological_process
plasma membrane organization and biogenesis
GO:0007009
plasma membrane organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.
GOC:dph
GOC:jl
GOC:mah
plasma membrane organisation
GOC:curators
plasma membrane organization and biogenesis
GOC:mah
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
MIPS_funcat:42.04
cytoskeleton organisation
biological_process
cytoskeletal organization and biogenesis
cytoskeletal regulator activity
cytoskeleton organization and biogenesis
GO:0007010
cytoskeleton organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
GOC:dph
GOC:jl
GOC:mah
cytoskeleton organisation
GOC:curators
cytoskeletal organization and biogenesis
GOC:mah
cytoskeleton organization and biogenesis
GOC:mah
The directed movement of substances into, out of or within a vacuole.
MIPS_funcat:20.09.13
biological_process
GO:0007034
vacuolar transport
The directed movement of substances into, out of or within a vacuole.
GOC:ai
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
MIPS_funcat:10
MIPS_funcat:10.03
Wikipedia:Cell_cycle
cell-division cycle
biological_process
GO:0007049
cell cycle
The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
GOC:go_curators
GOC:mtg_cell_cycle
The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
MIPS_funcat:10.03.04
MIPS_funcat:10.03.04.05
Wikipedia:Chromosome_segregation
chromosome division
biological_process
chromosome transmission
GO:0007059
chromosome segregation
The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
GOC:jl
GOC:mah
GOC:mtg_cell_cycle
GOC:vw
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
davidos
2014-04-15T15:59:10Z
GO:0098602
MIPS_funcat:34.07
Wikipedia:Cell_adhesion
biological_process
cell adhesion molecule activity
single organism cell adhesion
GO:0007155
cell adhesion
The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
GOC:hb
GOC:pf
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
GO:0023033
MIPS_funcat:30
Wikipedia:Signal_transduction
signaling cascade
signalling cascade
biological_process
signaling pathway
signalling pathway
GO:0007165
Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not.
signal transduction
The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
GOC:go_curators
GOC:mtg_signaling_feb11
signalling pathway
GOC:mah
Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
cell-cell signalling
biological_process
GO:0007267
cell-cell signaling
Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
GOC:dos
GOC:mah
A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
GO:0016280
Wikipedia:Aging
ageing
biological_process
GO:0007568
aging
A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
GOC:PO_curators
Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
molecular_function
GO:0008092
cytoskeletal protein binding
Interacting selectively and non-covalently with any protein component of any cytoskeleton (actin, microtubule, or intermediate filament cytoskeleton).
GOC:mah
Interacting selectively and non-covalently with a transcription factor, a protein required to initiate or regulate transcription.
TF binding
molecular_function
GO:0008134
transcription factor binding
Interacting selectively and non-covalently with a transcription factor, a protein required to initiate or regulate transcription.
ISBN:0198506732
Functions during translation by interacting selectively and non-covalently with RNA during polypeptide synthesis at the ribosome.
translation factor activity, nucleic acid binding
molecular_function
GO:0008135
translation factor activity, RNA binding
Functions during translation by interacting selectively and non-covalently with RNA during polypeptide synthesis at the ribosome.
GOC:ai
GOC:vw
translation factor activity, nucleic acid binding
GOC:mah
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
janelomax
2012-09-19T15:05:24Z
GO:0000004
GO:0007582
GO:0044699
Wikipedia:Biological_process
biological process
physiological process
biological_process
single organism process
single-organism process
GO:0008150
Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this.
biological_process
A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence.
GOC:pdt
Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0004480
methylase
EC:2.1.1
Reactome:R-HSA-379387
Reactome:R-HSA-379464
Reactome:R-HSA-6800149
Reactome:R-HSA-71286
molecular_function
GO:0008168
methyltransferase activity
Catalysis of the transfer of a methyl group to an acceptor molecule.
ISBN:0198506732
Reactome:R-HSA-379387
methylation of Dopamine to form 3-Methoxytyramine
Reactome:R-HSA-379464
Methylation of 3,4-dihydroxyphenylacetic acid to homovanillic acid
Reactome:R-HSA-6800149
N6AMT1:TRMT112 transfers CH3 group from AdoMet to MMAIII
Reactome:R-HSA-71286
guanidinoacetate + S-adenosylmethionine => creatine + S-adenosylhomocysteine
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
MIPS_funcat:40.10
biological_process
accidental cell death
necrosis
GO:0008219
This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term.
cell death
Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538).
GOC:mah
GOC:mtg_apoptosis
PMID:25236395
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
EC:3.4
Reactome:R-HSA-205112
Reactome:R-HSA-3000243
Reactome:R-HSA-3139027
Reactome:R-HSA-376149
Reactome:R-HSA-448678
Reactome:R-HSA-5655483
Reactome:R-HSA-5684864
Reactome:R-HSA-5685902
Reactome:R-HSA-5693319
hydrolase, acting on peptide bonds
peptide hydrolase activity
protease activity
proteinase activity
molecular_function
GO:0008233
peptidase activity
Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
GOC:jl
ISBN:0815332181
Reactome:R-HSA-205112
gamma-secretase cleaves p75NTR, releasing NRIF and TRAF6
Reactome:R-HSA-3000243
Unknown protease degrades GIF:Cbl to release Cbl
Reactome:R-HSA-3139027
Maturation of HIV Virion
Reactome:R-HSA-376149
Proteolytic processing of SLIT
Reactome:R-HSA-448678
CTSG cleaves CASP1(1-404)
Reactome:R-HSA-5655483
USP1 autocleavage
Reactome:R-HSA-5684864
NAPSA, CTSH, PGA3-5 cleave pro-SFTPB
Reactome:R-HSA-5685902
NAPSA, CTSH, PGA3-5 cleave pro-SFTPC
Reactome:R-HSA-5693319
CTRC hydrolyses PRSS1
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
biological_process
cell proliferation
GO:0008283
This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms.
cell population proliferation
The multiplication or reproduction of cells, resulting in the expansion of a cell population.
GOC:mah
GOC:mb
Interacting selectively and non-covalently with a lipid.
MIPS_funcat:16.09
molecular_function
GO:0008289
lipid binding
Interacting selectively and non-covalently with a lipid.
GOC:ai
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
janelomax
2012-10-17T15:52:35Z
GO:0044243
GO:0044712
Wikipedia:Catabolism
breakdown
catabolism
degradation
multicellular organismal catabolic process
biological_process
single-organism catabolic process
GO:0009056
catabolic process
The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism.
ISBN:0198547684
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
janelomax
2012-10-17T15:52:18Z
GO:0044274
GO:0044711
formation
Wikipedia:Anabolism
anabolism
biosynthesis
synthesis
multicellular organismal biosynthetic process
biological_process
single-organism biosynthetic process
GO:0009058
biosynthetic process
The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
GOC:curators
ISBN:0198547684
Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
MIPS_funcat:70.26
Wikipedia:Plastid
cellular_component
GO:0009536
plastid
Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
GOC:jl
ISBN:0198547684
A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
Wikipedia:Thylakoid
cellular_component
photosynthetic membrane
GO:0009579
A thylakoid is not considered an organelle, but some thylakoids are part of organelles.
thylakoid
A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.
GOC:ds
GOC:mtg_sensu
ISBN:0198506732
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
GO:0009795
embryogenesis and morphogenesis
Wikipedia:Embryogenesis
embryogenesis
embryonal development
biological_process
GO:0009790
embryo development
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
GOC:go_curators
GOC:isa_complete
GOC:mtg_sensu
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GO:0015831
MIPS_funcat:14
MIPS_funcat:14.04
MIPS_funcat:20.01.10
enzyme transport
biological_process
GO:0015031
protein transport
The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
GOC:ai
The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
MIPS_funcat:02.30
Wikipedia:Photosynthesis
biological_process
GO:0015979
photosynthesis
The synthesis by organisms of organic chemical compounds, especially carbohydrates, from carbon dioxide (CO2) using energy obtained from light rather than from the oxidation of chemical compounds.
ISBN:0198547684
A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
GO:0006899
MIPS_funcat:20.09.07
vesicle transport
vesicular transport
nonselective vesicle transport
biological_process
protein sorting along secretory pathway
vesicle trafficking
GO:0016192
vesicle-mediated transport
A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
GOC:ai
GOC:mah
ISBN:08789310662000
vesicular transport
GOC:mah
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
Reactome:R-HSA-6788855
Reactome:R-HSA-6788867
phosphokinase activity
molecular_function
GO:0016301
Note that this term encompasses all activities that transfer a single phosphate group; although ATP is by far the most common phosphate donor, reactions using other phosphate donors are included in this term.
kinase activity
Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
ISBN:0198506732
Reactome:R-HSA-6788855
FN3KRP phosphorylates PsiAm, RibAm
Reactome:R-HSA-6788867
FN3K phosphorylates ketosamines
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
EC:1
Reactome:R-HSA-1614362
Reactome:R-HSA-209921
Reactome:R-HSA-209960
Reactome:R-HSA-3095889
Reactome:R-HSA-390425
Reactome:R-HSA-390438
Reactome:R-HSA-5662660
Reactome:R-HSA-8878581
Reactome:R-HSA-8936442
Reactome:R-HSA-9020249
Reactome:R-HSA-9020260
Reactome:R-HSA-9024624
Reactome:R-HSA-9024630
Reactome:R-HSA-9025007
Reactome:R-HSA-9026001
Reactome:R-HSA-9026917
Reactome:R-HSA-9027033
redox activity
oxidoreductase activity, acting on other substrates
molecular_function
GO:0016491
Note that enzymes of class EC:1.97.-.- should also be annotated to this term.
oxidoreductase activity
Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
GOC:go_curators
Reactome:R-HSA-1614362
SUMF1 mediates the oxidation of cysteine to formylglycine, producing active arylsulfatases
Reactome:R-HSA-209921
Monoiodinated tyrosine can be deiodinated
Reactome:R-HSA-209960
Diiodinated tyrosine can be deiodinated
Reactome:R-HSA-3095889
MMACHC reduces Cbl
Reactome:R-HSA-390425
FAR1 reduces PalmCoA to HXOL
Reactome:R-HSA-390438
FAR2 reduces PalmCoA to HXOL
Reactome:R-HSA-5662660
Dopachrome is transformed to DHICA by DCT
Reactome:R-HSA-8878581
TYRP1 oxidises DHICA to IQCA
Reactome:R-HSA-8936442
MARC1,MARC2 reduce N-hydroxylated compounds
Reactome:R-HSA-9020249
Hydroperoxy reductase reduces 4(S)-Hp-17(S)-HDHA to RvD6
Reactome:R-HSA-9020260
Hydroperoxy reducatse reduces 7(S)-Hp-17(S)-HDHA to RvD5
Reactome:R-HSA-9024624
Hydroperoxy reductase reduces 4(S)-Hp-17(R)-HDHA to AT-RvD6
Reactome:R-HSA-9024630
Hydroperoxy reductase reduces 7(S)-Hp-17(R)-HDHA to AT-RvD5
Reactome:R-HSA-9025007
Hydroperoxy reductase reduces 7(S),14(S)-diHp-DHA to 7-epi-MaR1
Reactome:R-HSA-9026001
Hydroperoxy reductase reduces 7,17-diHp-DPAn-3 to RvD5n-3DPA
Reactome:R-HSA-9026917
Lipoxygenase dehydrogenates 7(S),17(S)-diHp-DHA to 7S(8)-epoxy-17(S)-HDHA
Reactome:R-HSA-9027033
Hydroperoxy reducatase reduces 14(S)-Hp-DHA to 14(S)-HDHA
Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
GO:0008415
EC:2.3
Reactome:R-HSA-159431
Reactome:R-HSA-192312
Reactome:R-HSA-193491
Reactome:R-HSA-6792572
Reactome:R-HSA-8858298
acyltransferase activity
molecular_function
GO:0016746
transferase activity, transferring acyl groups
Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
GOC:jl
ISBN:0198506732
Reactome:R-HSA-159431
Cytosolic chenodeoxycholoyl-CoA or choloyl-CoA are conjugated with glycine or taurine
Reactome:R-HSA-192312
Choloyl CoA reacts with glycine or taurine to form glycocholate or taurocholate
Reactome:R-HSA-193491
Chenodeoxycholoyl CoA reacts with glycine or taurine to form glycochenodeoxycholate or taurochenodeoxycholate
Reactome:R-HSA-6792572
LIPT1 transfers lipoyl group from lipoyl-GCSH to DHs
Reactome:R-HSA-8858298
HRASLS transfer acyl group from PC to PE to form NAPE
Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
GO:0016932
EC:2.4
Reactome:R-HSA-5173005
Reactome:R-HSA-6785565
glycosyltransferase activity
transglycosidase activity
transglycosylase activity
transferase activity, transferring other glycosyl groups
molecular_function
GO:0016757
Note that enzymes of class EC:2.4.99.- should also be annotated to this term.
transferase activity, transferring glycosyl groups
Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
GOC:jl
ISBN:0198506732
Reactome:R-HSA-5173005
B3GALTL transfers glucose to O-fucosyl-proteins
Reactome:R-HSA-6785565
Defective B3GALTL does not transfer glucose to O-fucosyl-proteins
Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
GO:0016766
EC:2.5
EC:2.5.1
Reactome:R-HSA-4419978
Reactome:R-HSA-4755545
Reactome:R-HSA-6782893
transferase activity, transferring alkyl or aryl groups, other than methyl groups
molecular_function
GO:0016765
transferase activity, transferring alkyl or aryl (other than methyl) groups
Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).
GOC:jl
ISBN:0198506732
Reactome:R-HSA-4419978
DHDDS:NUS1 elongates E,E-FPP with (n)IPPP to form pPPP
Reactome:R-HSA-4755545
Defective DHDDS does not elongate E,E-FPP
Reactome:R-HSA-6782893
TRMT12 transforms yW-187 yielding yW-86 at nucleotide 37 of tRNA(Phe)
Catalysis of the transfer of a nucleotidyl group to a reactant.
EC:2.7.7
Reactome:R-HSA-6782434
molecular_function
GO:0016779
nucleotidyltransferase activity
Catalysis of the transfer of a nucleotidyl group to a reactant.
ISBN:0198506732
Reactome:R-HSA-6782434
THG1L transfers GMP to 5' end of tRNA(His)
Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
GO:0003869
GO:0016302
EC:3.1.3
MetaCyc:4-NITROPHENYLPHOSPHATASE-RXN
RHEA:21664
Reactome:R-HSA-4419986
phosphoric monoester hydrolase activity
4-nitrophenylphosphatase activity
4-nitrophenylphosphate phosphohydrolase activity
K-pNPPase activity
NPPase activity
PNPPase activity
ecto-p-nitrophenyl phosphatase activity
nitrophenyl phosphatase activity
p-nitrophenylphosphatase activity
p-nitrophenylphosphate phosphohydrolase activity
para-nitrophenyl phosphatase activity
molecular_function
phosphatase
GO:0016791
phosphatase activity
Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
EC:3.1.3
GOC:curators
GOC:pg
Reactome:R-HSA-4419986
Unknown pPPP phosphatase dephosphorylates pPPP to pPNOL
4-nitrophenylphosphate phosphohydrolase activity
EC:3.1.3.41
K-pNPPase activity
EC:3.1.3.41
NPPase activity
EC:3.1.3.41
PNPPase activity
EC:3.1.3.41
ecto-p-nitrophenyl phosphatase activity
EC:3.1.3.41
nitrophenyl phosphatase activity
EC:3.1.3.41
p-nitrophenylphosphatase activity
EC:3.1.3.41
p-nitrophenylphosphate phosphohydrolase activity
EC:3.1.3.41
para-nitrophenyl phosphatase activity
EC:3.1.3.41
Catalysis of the hydrolysis of any glycosyl bond.
EC:3.2
Reactome:R-HSA-1793176
Reactome:R-HSA-2065233
glycosidase activity
N-glycosylase
glycosylase
molecular_function
GO:0016798
hydrolase activity, acting on glycosyl bonds
Catalysis of the hydrolysis of any glycosyl bond.
GOC:jl
Reactome:R-HSA-1793176
DS is cleaved from its proteoglycan
Reactome:R-HSA-2065233
CS is cleaved from its proteoglycan
Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
EC:3.5
Reactome:R-HSA-6803753
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in other compounds
molecular_function
GO:0016810
Note that enzymes of class EC:3.5.99.- should also be annotated to this term.
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
GOC:jl
Reactome:R-HSA-6803753
NAAA hydrolyses NAEs to FAs and ethanolamine
Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
EC:4
Reactome:R-HSA-5696408
Reactome:R-HSA-6782895
other lyase activity
molecular_function
GO:0016829
Note that enzymes of class EC:4.99.-.- should also be annotated to this term.
lyase activity
Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
EC:4.-.-.-
ISBN:0198547684
Reactome:R-HSA-5696408
PHYKPL tetramer hydrolyses 5PHL
Reactome:R-HSA-6782895
TYW1:FMN:4Fe-4S transforms 1-methylguanosine yielding yW-187 (4-demethylwyosine) at nucleotide 37 of tRNA(Phe)
Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
EC:5
Reactome:R-HSA-6787623
other isomerase activity
molecular_function
GO:0016853
Note that enzymes of class EC:5.99.-.- should also be annotated to this term.
isomerase activity
Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
ISBN:0198506732
Reactome:R-HSA-6787623
TSTA3 dimer epimerises GDP-DHDMan to GDP-KDGal
Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
EC:6
synthetase activity
molecular_function
GO:0016874
ligase activity
Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
EC:6
GOC:mah
synthetase activity
GOC:jh2
Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
GO:0004002
EC:3.6.1.3
MetaCyc:ADENOSINETRIPHOSPHATASE-RXN
RHEA:13065
Reactome:R-HSA-159101
Reactome:R-HSA-416985
Reactome:R-HSA-5654989
Reactome:R-HSA-5694425
Reactome:R-HSA-6809015
Reactome:R-HSA-6811422
Reactome:R-HSA-6814670
Reactome:R-HSA-6814678
Reactome:R-HSA-6814683
Reactome:R-HSA-72139
Reactome:R-HSA-8847638
Reactome:R-HSA-8868658
Reactome:R-HSA-917693
Reactome:R-HSA-9609860
ATP hydrolase activity
ATP monophosphatase activity
ATP phosphohydrolase activity
adenosine 5'-triphosphatase activity
adenosine triphosphatase activity
adenosinetriphosphatase activity
(Ca2+ + Mg2+)-ATPase
HCO3--ATPase
molecular_function
SV40 T-antigen
complex V (mitochondrial electron transport)
GO:0016887
ATPase activity
Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
EC:3.6.1.3
GOC:jl
Reactome:R-HSA-159101
NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)
Reactome:R-HSA-416985
Trafficking of GluR2-containing AMPA receptors to synapse
Reactome:R-HSA-5654989
SPRTN:VCP-mediated release of POLH from monoUb:K164-PCNA
Reactome:R-HSA-5694425
NSF ATPase activity dissociates cis-SNARE
Reactome:R-HSA-6809015
NSF ATPase activity dissociates cis-SNARE at cis-Golgi
Reactome:R-HSA-6811422
NSF ATPase activity dissociates cis-SNARE at the ER
Reactome:R-HSA-6814670
ATP hydrolysis by RHOBTB3 promotes PLIN3 dissociation
Reactome:R-HSA-6814678
ATP hydrolysis by NSF disassembles the cis-SNARE at the TGN
Reactome:R-HSA-6814683
NSF-dependent ATP hydrolysis disassembles the cis-SNARE at the TGN
Reactome:R-HSA-72139
Formation of the active Spliceosomal C (B*) complex
Reactome:R-HSA-8847638
ATP hydrolysis by NSF disassembles the cis-SNARE at the Golgi membrane
Reactome:R-HSA-8868658
HSPA8-mediated ATP hydrolysis promotes vesicle uncoating
Reactome:R-HSA-917693
ESCRT Disassembly
Reactome:R-HSA-9609860
Tail-anchored protein:SGTA:BAG6:GET4:UBL4A:ASNA1:ATP dissociates and ASNA1 hydrolyzes ATP yielding Tail-anchored protein:ASNA1:ADP
ATP hydrolase activity
EC:3.6.1.3
ATP monophosphatase activity
EC:3.6.1.3
adenosine 5'-triphosphatase activity
EC:3.6.1.3
adenosine triphosphatase activity
EC:3.6.1.3
(Ca2+ + Mg2+)-ATPase
EC:3.6.1.3
HCO3--ATPase
EC:3.6.1.3
SV40 T-antigen
EC:3.6.1.3
complex V (mitochondrial electron transport)
EC:3.6.1.3
The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients.
MIPS_funcat:01.20
Wikipedia:Secondary_metabolism
secondary metabolism
secondary metabolite metabolic process
secondary metabolite metabolism
biological_process
GO:0019748
secondary metabolic process
The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients.
GOC:go_curators
Interacting selectively and non-covalently with ribosomal RNA.
GO:0000944
base pairing with rRNA
molecular_function
GO:0019843
rRNA binding
Interacting selectively and non-covalently with ribosomal RNA.
GOC:jl
Interacting selectively and non-covalently with any enzyme.
molecular_function
GO:0019899
enzyme binding
Interacting selectively and non-covalently with any enzyme.
GOC:jl
A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state.
biological_process
GO:0021700
This term was added by GO_REF:0000021.
developmental maturation
A developmental process, independent of morphogenetic (shape) change, that is required for an anatomical structure, cell or cellular component to attain its fully functional state.
GOC:cls
GOC:dgh
GOC:dph
GOC:jid
GOC:mtg_15jun06
GO_REF:0000021
The aggregation, arrangement and bonding together of a cellular component.
GO:0071844
cell structure assembly
cellular component assembly at cellular level
biological_process
GO:0022607
cellular component assembly
The aggregation, arrangement and bonding together of a cellular component.
GOC:isa_complete
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
RNA-protein complex assembly
RNP complex assembly
protein-RNA complex assembly
biological_process
GO:0022618
ribonucleoprotein complex assembly
The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex.
GOC:jl
Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
GO:0005386
GO:0015563
GO:0015646
GO:0022891
GO:0022892
Reactome:R-HSA-1236947
Reactome:R-HSA-429036
Reactome:R-HSA-5638209
Reactome:R-HSA-5671707
Reactome:R-HSA-6784434
Reactome:R-HSA-6784436
substrate-specific transporter activity
molecular_function
substrate-specific transmembrane transporter activity
uptake permease activity
uptake transmembrane transporter activity
GO:0022857
transmembrane transporter activity
Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
GOC:jid
GOC:mtg_transport
ISBN:0815340729
Reactome:R-HSA-1236947
Egress of internalized antigen to the cytosol via sec61
Reactome:R-HSA-429036
SLC2A9 transports Fru, Glc, urate
Reactome:R-HSA-5638209
Defective SLC2A9 does not transport Fru, Glc, urate
Reactome:R-HSA-5671707
Fe3+ dissociates from SLC22A17:LCN2:2,5DHBA
Reactome:R-HSA-6784434
An unknown carrier transports cytosolic glyoxylate to the peroxisome
Reactome:R-HSA-6784436
An unknown carrier transports mitochondrial glyoxylate to the cytosol
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
MIPS_funcat:40.02
Wikipedia:Cellular_differentiation
biological_process
GO:0030154
cell differentiation
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
ISBN:0198506732
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
MIPS_funcat:42.27.01
extracellular matrix organisation
biological_process
extracellular matrix organization and biogenesis
GO:0030198
extracellular matrix organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
GOC:mah
extracellular matrix organisation
GOC:curators
extracellular matrix organization and biogenesis
GOC:mah
Binds to and modulates the activity of an enzyme.
GO:0010576
MIPS_funcat:18.02.01
catalytic regulator activity
enzyme modulator
metalloenzyme regulator activity
molecular_function
GO:0030234
GO:0030234 is reserved for cases when the regulator directly interacts with the enzyme. When regulation of enzyme activity is achieved without enzyme binding, or when the mechanism of regulation is unknown, instead annotate to 'regulation of catalytic activity ; GO:0050790'.
enzyme regulator activity
Binds to and modulates the activity of an enzyme.
GOC:dph
GOC:mah
GOC:tb
catalytic regulator activity
GOC:dph
A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space.
cellular_component
GO:0030312
The outer membrane (of gram negative bacteria) or cell wall (of yeast or Gram positive bacteria) are defined as parts of this structure, see 'external encapsulating structure part'.
external encapsulating structure
A structure that lies outside the plasma membrane and surrounds the entire cell or cells. This does not include the periplasmic space.
GOC:go_curators
The codon binding activity of a tRNA that positions an activated amino acid, mediating its insertion at the correct point in the sequence of a nascent polypeptide chain during protein synthesis.
molecular_function
tRNA
transfer RNA
GO:0030533
Note that this term can be used in place of the obsolete term 'transfer RNA ; GO:0005563'.
triplet codon-amino acid adaptor activity
The codon binding activity of a tRNA that positions an activated amino acid, mediating its insertion at the correct point in the sequence of a nascent polypeptide chain during protein synthesis.
GOC:hjd
GOC:mtg_MIT_16mar07
ISBN:0198506732
Specifies the site of a posttranscriptional modification in an RNA molecule by base pairing with a short sequence around the target residue.
molecular_function
GO:0030555
Note that this term describes the activity of a nucleic acid, usually RNA, gene product that interacts with other RNA molecules via base pairing; it should not be used to annotate proteins.
RNA modification guide activity
Specifies the site of a posttranscriptional modification in an RNA molecule by base pairing with a short sequence around the target residue.
GOC:mah
PMID:12457565
The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
protein-protein adaptor
molecular_function
GO:0030674
protein binding, bridging
The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
GOC:bf
GOC:mah
GOC:vw
The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell.
MIPS_funcat:20.09.14
biological_process
GO:0030705
cytoskeleton-dependent intracellular transport
The directed movement of substances along cytoskeletal fibers such as microfilaments or microtubules within a cell.
GOC:mah
A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
GO:0005578
MIPS_funcat:70.27.01
NIF_Subcellular:nlx_subcell_20090513
Wikipedia:Extracellular_matrix
proteinaceous extracellular matrix
matrisome
cellular_component
GO:0031012
extracellular matrix
A structure lying external to one or more cells, which provides structural support, biochemical or biomechanical cues for cells or tissues.
GOC:BHF
GOC:mah
GOC:rph
NIF_Subcellular:nlx_subcell_20090513
PMID:21123617
PMID:28089324
A vesicle found in the cytoplasm of a cell.
GO:0016023
NIF_Subcellular:sao180601769
cellular_component
cytoplasmic membrane bounded vesicle
cytoplasmic membrane-enclosed vesicle
cytoplasmic, membrane-bounded vesicle
GO:0031410
cytoplasmic vesicle
A vesicle found in the cytoplasm of a cell.
GOC:ai
GOC:mah
GOC:vesicles
Interacting selectively and non-covalently with a small conjugating protein such as ubiquitin or a ubiquitin-like protein.
small conjugating protein binding
molecular_function
GO:0032182
ubiquitin-like protein binding
Interacting selectively and non-covalently with a small conjugating protein such as ubiquitin or a ubiquitin-like protein.
GOC:mah
small conjugating protein binding
GOC:dph
Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites.
Wikipedia:Transposon
biological_process
GO:0032196
transposition
Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites.
GOC:jp
ISBN:1555812090
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
GO:0043234
macromolecular complex
macromolecule complex
protein containing complex
protein complex
protein-protein complex
cellular_component
GO:0032991
A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole.
protein-containing complex
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
GOC:dos
GOC:mah
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix.
cell junction assembly and maintenance
cell junction organisation
biological_process
cell junction biogenesis
GO:0034330
cell junction organization
A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a cell junction. A cell junction is a specialized region of connection between two cells or between a cell and the extracellular matrix.
GOC:dph
GOC:jl
GOC:mah
cell junction organisation
GOC:mah
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
cellular nitrogen compound metabolism
biological_process
GO:0034641
cellular nitrogen compound metabolic process
The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
GOC:mah
The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.
nucleobase, nucleoside, nucleotide and nucleic acid breakdown
nucleobase, nucleoside, nucleotide and nucleic acid catabolism
nucleobase, nucleoside, nucleotide and nucleic acid degradation
biological_process
nucleobase, nucleoside, nucleotide and nucleic acid catabolic process
GO:0034655
nucleobase-containing compound catabolic process
The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids.
GOC:mah
nucleobase, nucleoside, nucleotide and nucleic acid catabolic process
GOC:dph
GOC:tb
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO:0048590
biological_process
growth pattern
non-developmental growth
GO:0040007
See also the biological process term 'cell growth ; GO:0016049'.
growth
The increase in size or mass of an entire organism, a part of an organism or a cell.
GOC:bf
GOC:ma
non-developmental growth
GOC:mah
Self-propelled movement of a cell or organism from one location to another.
MIPS_funcat:02.45.11
biological_process
GO:0040011
locomotion
Self-propelled movement of a cell or organism from one location to another.
GOC:dgh
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
GO:0007046
ribosome biogenesis and assembly
biological_process
GO:0042254
ribosome biogenesis
A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
GOC:ma
PMID:26404467
Wikipedia:Ribosome_biogenesis
Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
molecular_function
histone-specific chaperone activity
GO:0042393
histone binding
Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
GOC:jl
Any biological process involved in the maintenance of an internal steady state.
GO:0032844
GO:0032845
GO:0032846
homeostasis
activation of homeostatic process
inhibition of homeostatic process
biological_process
negative regulation of homeostatic process
positive regulation of homeostatic process
regulation of homeostatic process
GO:0042592
homeostatic process
Any biological process involved in the maintenance of an internal steady state.
GOC:jl
ISBN:0395825172
Interacting selectively and non-covalently with ions, charged atoms or groups of atoms.
molecular_function
atom binding
GO:0043167
ion binding
Interacting selectively and non-covalently with ions, charged atoms or groups of atoms.
GOC:jl
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
NIF_Subcellular:sao1539965131
Wikipedia:Organelle
cellular_component
GO:0043226
organelle
Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane.
GOC:go_curators
The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
biological_process
GO:0043473
pigmentation
The accumulation of pigment in an organism, tissue or cell, either by increased deposition or by increased number of cells.
GOC:jl
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
jane
2010-01-26T12:05:20Z
small molecule metabolism
biological_process
GO:0044281
Small molecules in GO include monosaccharides but exclude disaccharides and polysaccharides.
small molecule metabolic process
The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.
GOC:curators
GOC:pde
GOC:vw
A process carried out by symbiont gene products that enables the interaction between two organisms living together in more or less intimate association. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.
GO:0043298
GO:0044404
GO:0072519
GO:0085031
commensalism
host-pathogen interaction
parasitism
biological_process
symbiosis
symbiosis, encompassing mutualism through parasitism
symbiotic interaction
symbiotic interaction between host and organism
symbiotic interaction between organisms
symbiotic interaction between species
GO:0044403
Changed term, definition see https://github.com/geneontology/go-ontology/issues/14807
symbiont process
A process carried out by symbiont gene products that enables the interaction between two organisms living together in more or less intimate association. The various forms of symbiosis include parasitism, in which the association is disadvantageous or destructive to one of the organisms; mutualism, in which the association is advantageous, or often necessary to one or both and not harmful to either; and commensalism, in which one member of the association benefits while the other is not affected. However, mutualism, parasitism, and commensalism are often not discrete categories of interactions and should rather be perceived as a continuum of interaction ranging from parasitism to mutualism. In fact, the direction of a symbiotic interaction can change during the lifetime of the symbionts due to developmental changes as well as changes in the biotic/abiotic environment in which the interaction occurs. Microscopic symbionts are often referred to as endosymbionts.
GOC:cc
https://study.com/academy/lesson/symbiont-definition-lesson-quiz.html
The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
formation of an anatomical structure involved in morphogenesis
biological_process
GO:0048646
Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense.
anatomical structure formation involved in morphogenesis
The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
GOC:dph
GOC:jid
GOC:tb
formation of an anatomical structure involved in morphogenesis
GOC:dph
GOC:tb
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
development of an anatomical structure
biological_process
GO:0048856
This term was added by GO_REF:0000021.
anatomical structure development
The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome.
GOC:mtg_15jun06
GO_REF:0000021
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
cell locomotion
movement of a cell
biological_process
cell movement
GO:0048870
cell motility
Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
GOC:dgh
GOC:dph
GOC:isa_complete
GOC:mlg
A organ system process carried out by any of the organs or tissues of neurological system.
MIPS_funcat:36.25.03
neurological system process
neurophysiological process
biological_process
pan-neural process
GO:0050877
Discussion of class label and synonyms: https://github.com/geneontology/go-ontology/issues/13824
nervous system process
A organ system process carried out by any of the organs or tissues of neurological system.
GOC:ai
GOC:mtg_cardio
Interacting selectively and non-covalently with an unfolded protein.
binding unfolded ER proteins
molecular_function
chaperone activity
fimbrium-specific chaperone activity
glycoprotein-specific chaperone activity
histone-specific chaperone activity
ribosomal chaperone activity
tubulin-specific chaperone activity
GO:0051082
unfolded protein binding
Interacting selectively and non-covalently with an unfolded protein.
GOC:ai
The chemical reactions and pathways involving a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
cofactor metabolism
biological_process
GO:0051186
cofactor metabolic process
The chemical reactions and pathways involving a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
GOC:ai
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
GO:0007001
GO:0051277
MIPS_funcat:42.10.03
chromosome organisation
biological_process
chromosome organization and biogenesis
maintenance of genome integrity
nuclear genome maintenance
GO:0051276
chromosome organization
A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
GOC:ai
GOC:dph
GOC:jl
GOC:mah
chromosome organization and biogenesis
GOC:mah
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
Wikipedia:Cell_division
biological_process
GO:0051301
Note that this term differs from 'cytokinesis ; GO:0000910' in that cytokinesis does not include nuclear division.
cell division
The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
GOC:di
GOC:go_curators
GOC:pr
Any process leading to the attainment of the full functional capacity of a protein.
biological_process
GO:0051604
protein maturation
Any process leading to the attainment of the full functional capacity of a protein.
GOC:ai
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
tanyaberardini
2015-10-21T13:22:47Z
GO:0090662
membrane transport
ATP hydrolysis coupled transmembrane transport
biological_process
GO:0055085
Transmembrane transport is the transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes.
transmembrane transport
The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
GOC:dph
GOC:jid
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
janelomax
2010-02-08T02:43:11Z
GO:0016044
GO:0044802
cellular membrane organisation
cellular membrane organization
membrane organisation
biological_process
membrane organization and biogenesis
single-organism membrane organization
GO:0061024
membrane organization
A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
GOC:dph
GOC:tb
cellular membrane organisation
GOC:curators
membrane organisation
GOC:mah
membrane organization and biogenesis
GOC:mah
The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
GO:0006461
biological_process
chaperone activity
macromolecular complex assembly
macromolecule complex assembly
protein complex assembly
protein complex formation
GO:0065003
protein-containing complex assembly
The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex.
GOC:jl
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cell wall.
midori
2010-01-13T03:19:38Z
GO:0070882
cell wall organisation or biogenesis
cell wall organization or biogenesis at cellular level
cellular cell wall organisation or biogenesis
cellular cell wall organization or biogenesis
biological_process
GO:0071554
cell wall organization or biogenesis
A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cell wall.
GOC:mah
cell wall organisation or biogenesis
GOC:mah
cell wall organization or biogenesis at cellular level
GOC:mah
cellular cell wall organisation or biogenesis
GOC:mah
A nitrogen compound metabolic process that contributes to the nitrogen cycle. The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization.
midori
2010-09-30T05:21:03Z
Wikipedia:Nitrogen_cycle
biological_process
GO:0071941
nitrogen cycle metabolic process
A nitrogen compound metabolic process that contributes to the nitrogen cycle. The nitrogen cycle is a series of metabolic pathways by which nitrogen is converted between various forms and redox states; it encompasses pathways in which nitrogen is acted upon directly, such as nitrification, denitrification, nitrogen fixation, and mineralization.
GOC:mah
PMID:16675690
Wikipedia:Nitrogen_cycle
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
pg
2017-03-23T14:44:23Z
biological_process
GO:0140014
mitotic nuclear division
A mitotic cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
ISBN:0198547684