LiteFold/GO huggingface dataset:
obsolete zf-TRAF domain-mediated complex assembly (GO:0071534)
Namespace: biological_process
Definition: OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a TRAF-type zinc finger (zf-TRAF) domain interaction.
Synonyms: TRAF-type zinc finger domain-mediated complex assembly; zinc finger TRAF-type domain-mediated complex assembly; zinc-finger-TRAF domain-mediated complex assembly
Comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
RING-like zinc finger domain binding (GO:0071535)
Namespace: molecular_function
Definition: Binding to a RING-like zinc finger domain domain of a protein. The RING-like domain is a zinc finger domain that is related to the C3HC4 RING finger domain.
obsolete C3HC4-type RING finger domain-mediated complex assembly (GO:0071537)
Namespace: biological_process
Definition: OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a C3HC4-type RING finger domain interaction.
Synonyms: zinc finger C3HC4 type domain-mediated complex assembly
Comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
obsolete SH2 domain-mediated complex assembly (GO:0071538)
Namespace: biological_process
Definition: OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by an SH2 domain interaction.
Comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
eukaryotic translation initiation factor 3 complex, eIF3e (GO:0071540)
Namespace: cellular_component
Definition: An eukaryotic translation initiation factor 3 complex that contains the PCI-domain protein eIF3e.
Synonyms: eIF3e-containing eukaryotic translation initiation factor 3 complex
eukaryotic translation initiation factor 3 complex, eIF3m (GO:0071541)
Namespace: cellular_component
Definition: An eukaryotic translation initiation factor 3 complex that contains the PCI-domain protein eIF3m.
Synonyms: eIF3m-containing eukaryotic translation initiation factor 3 complex
dopaminergic neuron differentiation (GO:0071542)
Namespace: biological_process
Definition: The process in which a neuroblast acquires the specialized structural and functional features of a dopaminergic neuron, a neuron that secretes dopamine.
diphosphoinositol polyphosphate metabolic process (GO:0071543)
Namespace: biological_process
Definition: The chemical reactions and pathways involving a diphosphoinositol polyphosphate, 1,2,3,4,5,6-cyclohexanehexol with one or more diphosphate groups and multiple monophosphate groups attached.
Synonyms: diphosphoinositol polyphosphate metabolism
diphosphoinositol polyphosphate catabolic process (GO:0071544)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a diphosphoinositol polyphosphate, 1,2,3,4,5,6-cyclohexanehexol with one or more diphosphate groups and multiple monophosphate groups attached.
Synonyms: diphosphoinositol polyphosphate breakdown; diphosphoinositol polyphosphate catabolism; diphosphoinositol polyphosphate degradation
inositol phosphate catabolic process (GO:0071545)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of an inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
Synonyms: inositol phosphate breakdown; inositol phosphate catabolism; inositol phosphate degradation; myo-inositol phosphate catabolic process
pi-body (GO:0071546)
Namespace: cellular_component
Definition: A P granule that contains the PIWIL2-TDRD1 module, a set of proteins that act in the primary piRNA pathway. The pi-body corresponds to the cementing material between mitochondria found in gonocytes.
Synonyms: intermitochondrial cement
piP-body (GO:0071547)
Namespace: cellular_component
Definition: A P granule that contains the PIWIL4-TDRD9 module, a set of proteins that act in the secondary piRNA pathway.
response to dexamethasone (GO:0071548)
Namespace: biological_process
Definition: 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 dexamethasone stimulus.
Synonyms: response to dexamethasone stimulus
death-inducing signaling complex assembly (GO:0071550)
Namespace: biological_process
Definition: A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a death domain (DD) interaction, as part of the extrinsic apoptotic signaling pathway.
Synonyms: DD-mediated complex assembly; death domain-mediated complex assembly; death domain-mediated complex assembly involved in extrinsic apoptotic pathway; death-inducing signaling complex formation; death-inducing signalling complex assembly; DISC assembly; DISC formation
obsolete RIP homotypic interaction motif-mediated complex assembly (GO:0071552)
Namespace: biological_process
Definition: OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by a RIP homotypic interaction motif (RHIM) interaction.
Synonyms: RHIM-mediated complex assembly
Comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
G protein-coupled pyrimidinergic nucleotide receptor activity (GO:0071553)
Namespace: molecular_function
Definition: Combining with a pyrimidine nucleotide and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
Synonyms: G protein coupled pyrimidinergic nucleotide receptor activity; G-protein coupled pyrimidinergic nucleotide receptor activity; pyrimidinergic nucleotide receptor activity, G protein coupled; pyrimidinergic nucleotide receptor activity, G-protein coupled
cell wall organization (GO:0071555)
Namespace: biological_process
Definition: A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
Synonyms: cell wall organisation; cell wall organisation in other organism; cell wall organization and biogenesis; cell wall organization at cellular level; cell wall organization in other organism; cellular cell wall organisation; cellular cell wall organization
obsolete integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)
Namespace: cellular_component
Definition: OBSOLETE. The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
Synonyms: integral to ER membrane, lumenal side; integral to lumenal leaflet of endoplasmic reticulum membrane; integral to lumenal side of endoplasmic reticulum membrane; integral to lumenal side of ER membrane
Comment: This term was obsoleted because it represents protein topology, not a cellular component.
obsolete histone H3-K27 demethylation (GO:0071557)
Namespace: biological_process
Definition: OBSOLETE. The modification of histone H3 by the removal of a methyl group from lysine at position 27 of the histone.
Synonyms: H3K27 demethylation
Comment: This term was obsoleted because it represents a molecular function.
histone H3K27me2/H3K27me3 demethylase activity (GO:0071558)
Namespace: molecular_function
Definition: Catalysis of the removal of a methyl group from a tri- or a dimethyl-lysine residue at position 27 of the histone H3 protein. This is a dioxygenase reaction that is dependent on Fe(II) and 2-oxoglutarate.
Synonyms: histone demethylase activity (H3-K27 specific); histone H3-tri/di-methyl-lysine-27 demethylase activity; histone H3K27me2 demethylase activity; histone H3K27me3 demethylase activity
Comment: Comment: Note that the residue position corresponds to the canonical human H3 histone (UniProtKB:P84243); this residue is conserved across all eukaryotes. Residue 1 is the first residue following removal of the initiating Methionine (Met). Note that each histone is encoded by multiple genes, and sequences may vary across different genes within an organism.
response to transforming growth factor beta (GO:0071559)
Namespace: biological_process
Definition: 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 transforming growth factor beta stimulus.
Synonyms: response to TGF-beta stimulus; response to TGFbeta stimulus; response to transforming growth factor beta stimulus
cellular response to transforming growth factor beta stimulus (GO:0071560)
Namespace: biological_process
Definition: Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus.
Synonyms: cellular response to TGF-beta stimulus; cellular response to TGFbeta stimulus
nucleus-vacuole junction (GO:0071561)
Namespace: cellular_component
Definition: An organelle membrane contact site formed between the vacuole membrane and the outer nuclear membrane. In S. cerevisiae these contacts are mediated through direct physical interaction between Vac8p and Nvj1p.
Synonyms: nucleus-vacuole membrane contact site; NV junction; NVJ
nucleus-vacuole junction assembly (GO:0071562)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a set of components to form a nucleus-vacuole junction (NVJ), membrane contact sites formed between the vacuole membrane and the outer nuclear membrane. In S. cerevisiae these contacts are mediated through direct physical interaction between Vac8p and Nvj1p. The NVJ plays roles in piecemeal microautophagy of the nucleus and in the cytoplasm-to-vacuole targeting pathway.
Synonyms: nucleus-vacuole junction formation; NV junction assembly; NV junction formation; NVJ assembly; NVJ formation
Myo2p-Vac17p-Vac8p transport complex (GO:0071563)
Namespace: cellular_component
Definition: A protein complex that is involved in transport of vacuoles to a newly formed daughter cell. In yeast, this complex is composed of Myo2p, Vac17p, and Vac8p.
npBAF complex (GO:0071564)
Namespace: cellular_component
Definition: A SWI/SNF-type complex that is found in neural stem or progenitor cells, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A genes. The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells.
nBAF complex (GO:0071565)
Namespace: cellular_component
Definition: A SWI/SNF-type complex that is found in post-mitotic neurons, and in human contains actin and proteins encoded by the ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, DPF1/BAF45B, DPF3/BAF45C, ACTL6B/BAF53B genes. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth.
UFM1 activating enzyme activity (GO:0071566)
Namespace: molecular_function
Definition: Catalysis of the activation of the small ubiquitin-related modifier UFM1, through the formation of an ATP-dependent high-energy thiolester bond.
deUFMylase activity (GO:0071567)
Namespace: molecular_function
Definition: A thiol-dependent isopeptidase activity that cleaves UFM1 from a target protein to which it is conjugated.
Synonyms: UFM1 hydrolase activity
UFM1 transferase activity (GO:0071568)
Namespace: molecular_function
Definition: Catalysis of the transfer of UFM1 from one protein to another via the reaction X-UFM1 + Y = Y-UFM1 + X, where both X-UFM1 and Y-UFM1 are covalent linkages.
protein ufmylation (GO:0071569)
Namespace: biological_process
Definition: Covalent attachment of the ubiquitin-like protein UFM1 to another protein.
cement gland development (GO:0071570)
Namespace: biological_process
Definition: The process whose specific outcome is the progression of the cement gland over time, from its formation to the mature structure. The cement gland is a simple mucus-secreting organ positioned at the anterior of amphibious embryos. The cement gland attaches the newly hatched embryo to a support before the hatchling can swim well or feed.
obsolete LRR domain-mediated complex assembly (GO:0071571)
Namespace: biological_process
Definition: OBSOLETE. A process of protein complex assembly in which the arrangement and bonding together of the set of components that form the protein complex is mediated by an LRR (leucine-rich repeat) domain interaction.
Synonyms: leucine-rich repeat domain-mediated complex assembly
Comment: This term was obsoleted because it represented a molecular function (binding), not a biological process. The term represented a domain involved in protein-protein interactions, but no necessarily the process of assembling a complex.
obsolete histone H3-K56 deacetylation (GO:0071572)
Namespace: biological_process
Definition: OBSOLETE. The modification of histone H3 by the removal of an acetyl group from lysine at position 56 of the histone.
Comment: This term was obsoleted because it represents a molecular function.
shelterin complex assembly (GO:0071573)
Namespace: biological_process
Definition: The aggregation, arrangement and bonding together of a set of components to form a shelterin complex. A shelterin complex is a nuclear telomere cap complex that is formed by the association of telomeric ssDNA- and dsDNA-binding proteins with telomeric DNA, and is involved in telomere protection and recruitment of telomerase.
Synonyms: Pot1 complex assembly; Pot1-Tpz1 complex assembly; shelterin complex formation; telosome assembly
protein localization to medial cortex (GO:0071574)
Namespace: biological_process
Definition: A process in which a protein is transported to, or maintained in, the medial cortex.
Synonyms: protein localisation to medial cortex
obsolete integral component of external side of plasma membrane (GO:0071575)
Namespace: cellular_component
Definition: OBSOLETE. The component of the plasma membrane consisting of the gene products that penetrate only the external side of the membrane.
Synonyms: integral to external leaflet of plasma membrane; integral to external side of plasma membrane
Comment: This term was obsoleted because it represents protein topology, not a cellular component.
tetrahydrodictyopterin binding (GO:0071576)
Namespace: molecular_function
Definition: Binding to tetrahydrodictyopterin, the pterin 2-amino-6-[(1R,2R)-1,2-dihydroxypropyl]-5,6,7,8-tetrahydropteridin-4(3H)-one.
Synonyms: D-threo-tetrahydrobiopterin; DH4 binding
zinc ion transmembrane transport (GO:0071577)
Namespace: biological_process
Definition: A process in which a zinc II ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
Synonyms: zinc II ion transmembrane transport; zinc ion membrane transport; zinc transmembrane transport
Comment: Note that this term is not intended for use in annotating lateral movement within membranes.
zinc ion import across plasma membrane (GO:0071578)
Namespace: biological_process
Definition: The directed movement of zinc(2+) ions from outside of a cell, across the plasma membrane and into the cytosol.
Synonyms: high-affinity zinc II ion transmembrane import; high-affinity zinc II ion transport; low-affinity zinc II ion transport; zinc II ion plasma membrane import; zinc II ion transmembrane import; zinc import; zinc ion import into cell; zinc ion transmembrane import; zinc uptake
regulation of zinc ion transport (GO:0071579)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the directed movement of zinc ions (Zn2+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
regulation of zinc ion transmembrane transport (GO:0071580)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of the directed movement of zinc ions (Zn2+) from one side of a membrane to the other.
Synonyms: regulation of zinc ion membrane transport
regulation of zinc ion transmembrane import (GO:0071581)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate or extent of zinc ion import.
negative regulation of zinc ion transport (GO:0071582)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of zinc ions (Zn2+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
negative regulation of zinc ion transmembrane transport (GO:0071583)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of zinc ions (Zn2+) from one side of a membrane to the other.
Synonyms: negative regulation of zinc ion membrane transport
negative regulation of zinc ion transmembrane import (GO:0071584)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate or extent of zinc ion import.
detoxification of cadmium ion (GO:0071585)
Namespace: biological_process
Definition: Any process that reduces or removes the toxicity of cadmium ion. These may include transport of cadmium away from sensitive areas and to compartments or complexes whose purpose is sequestration of cadmium ion.
CAAX-box protein processing (GO:0071586)
Namespace: biological_process
Definition: The second process in a series of specific posttranslational modifications to the CAAX box region of CAAX box proteins, in which the last three amino acids of the protein (AAX) are removed by proteolysis.
obsolete CAAX-box protein modification (GO:0071587)
Namespace: biological_process
Definition: OBSOLETE. The covalent alteration of one or more amino acid residues within the CAAX box region of CAAX box proteins.
Comment: This term was obsoleted because it represents a molecular function.
hydrogen peroxide mediated signaling pathway (GO:0071588)
Namespace: biological_process
Definition: The series of molecular signals mediated by the detection of hydrogen peroxide (H2O2).
Synonyms: H2O2 mediated signaling pathway; hydrogen peroxide mediated signalling pathway
pyridine nucleoside biosynthetic process (GO:0071589)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of any pyridine nucleoside, one of a family of organic molecules consisting of a pyridine base covalently bonded to a sugar, usually ribose.
Synonyms: pyridine nucleoside anabolism; pyridine nucleoside biosynthesis; pyridine nucleoside formation; pyridine nucleoside synthesis
nicotinamide riboside biosynthetic process (GO:0071590)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of nicotinamide riboside, the product of the formation of a glycosidic bond between ribose and nicotinamide.
Synonyms: N-ribosylnicotinamide biosynthetic process; nicotinamide riboside anabolism; nicotinamide riboside biosynthesis; nicotinamide riboside formation; nicotinamide riboside synthesis
obsolete nicotinic acid riboside metabolic process (GO:0071591)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways involving nicotinic acid riboside, the product of the formation of a glycosidic bond between ribose and nicotinic acid.
Synonyms: D-ribosylnicotinic acid metabolic process; nicotinic acid riboside metabolism
Comment: This term was obsoleted because it is an unnecessary grouping class.
nicotinic acid riboside biosynthetic process (GO:0071592)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of nicotinic acid riboside, the product of the formation of a glycosidic bond between ribose and nicotinic acid.
Synonyms: D-ribosylnicotinic acid biosynthetic process; nicotinic acid riboside anabolism; nicotinic acid riboside biosynthesis; nicotinic acid riboside formation; nicotinic acid riboside synthesis
lymphocyte aggregation (GO:0071593)
Namespace: biological_process
Definition: The adhesion of one lymphocyte to one or more other lymphocytes via adhesion molecules.
thymocyte aggregation (GO:0071594)
Namespace: biological_process
Definition: The adhesion of one thymocyte (an immature T cell) to one or more other thymocytes via adhesion molecules.
Synonyms: immature T cell aggregation; immature T-cell aggregation; immature T-lymphocyte aggregation; T cell precursor aggregation; thymic lymphocyte aggregation
Nem1-Spo7 phosphatase complex (GO:0071595)
Namespace: cellular_component
Definition: A protein serine/threonine phosphatase complex that is involved in nuclear envelope organization, and contains proteins known in budding yeast as Nem1p and Spo7p.
ubiquitin-dependent protein catabolic process via the N-end rule pathway (GO:0071596)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the breakdown of a protein or peptide covalently tagged with ubiquitin, via the N-end rule pathway. In the N-end rule pathway, destabilizing N-terminal residues (N-degrons) in substrates are recognized by E3 ligases (N-recognins), whereupon the substrates are linked to ubiquitin and then delivered to the proteasome for degradation.
Synonyms: ubiquitin-dependent protein breakdown via the N-end rule pathway; ubiquitin-dependent protein catabolism via the N-end rule pathway; ubiquitin-dependent protein degradation via the N-end rule pathway
cellular birth scar (GO:0071597)
Namespace: cellular_component
Definition: Crater-like ring of chitinous scar tissue located on the surface of the daughter cell, in budding fungi, at the site of separation from the mother cell. It is formed after the newly emerged daughter cell separates, thereby marking the site of cytokinesis and septation.
neuronal ribonucleoprotein granule (GO:0071598)
Namespace: cellular_component
Definition: A ribonucleoprotein complex that is found in the cytoplasm of axons and dendrites, and transports translationally silenced mRNAs to dendritic synapses, where they are released and translated in response to specific exogenous stimuli.
Synonyms: neuronal RNA granule; neuronal RNP granule
otic vesicle development (GO:0071599)
Namespace: biological_process
Definition: The process whose specific outcome is the progression of the otic vesicle over time, from its formation to the mature structure. The otic vesicle is a transient embryonic structure formed during development of the vertebrate inner ear.
otic vesicle morphogenesis (GO:0071600)
Namespace: biological_process
Definition: The process in which the anatomical structures of the otic vesicle are generated and organized. The otic vesicle is a transient embryonic structure formed during development of the vertebrate inner ear.