LiteFold/GO huggingface dataset:
high-density lipoprotein particle remodeling (GO:0034375)
Namespace: biological_process
Definition: The acquisition, loss or modification of a protein or lipid within a high-density lipoprotein particle, including the hydrolysis of triglyceride by hepatic lipase, with the subsequent loss of free fatty acid, and the transfer of cholesterol esters from LDL to a triglyceride-rich lipoprotein particle by cholesteryl ester transfer protein (CETP), with the simultaneous transfer of triglyceride to LDL.
Synonyms: HDL remodeling; HDL remodelling; high-density lipoprotein particle remodelling
conversion of discoidal high-density lipoprotein particle to spherical high-density lipoprotein particle (GO:0034376)
Namespace: biological_process
Definition: The process in which a discoidal high-density lipoprotein (HDL) particle acquires additional lipid or protein molecules, and cholesterol in the particle is converted to tightly bound cholesterol esters by the action of phosphatidylcholine-sterol O-acyltransferase (lecithin cholesterol acyltransferase; LCAT), resulting in the formation of a spherical HDL particle.
Synonyms: conversion of discoidal HDL to spherical HDL; discoidal HDL remodeling; discoidal high-density lipoprotein remodeling
plasma lipoprotein particle assembly (GO:0034377)
Namespace: biological_process
Definition: The non-covalent aggregation and arrangement of proteins and lipids to form a plasma lipoprotein particle.
chylomicron assembly (GO:0034378)
Namespace: biological_process
Definition: The non-covalent aggregation and arrangement of proteins and lipids in the intestine to form a chylomicron.
very-low-density lipoprotein particle assembly (GO:0034379)
Namespace: biological_process
Definition: The non-covalent aggregation and arrangement of proteins and lipids in the liver to form a very-low-density lipoprotein particle.
Synonyms: VLDL assembly
high-density lipoprotein particle assembly (GO:0034380)
Namespace: biological_process
Definition: The non-covalent aggregation and arrangement of proteins and lipids to form a high-density lipoprotein particle.
Synonyms: HDL assembly
chylomicron remnant clearance (GO:0034382)
Namespace: biological_process
Definition: The process in which a chylomicron remnant is removed from the blood via receptor-mediated endocytosis into liver cells and its constituent parts degraded.
low-density lipoprotein particle clearance (GO:0034383)
Namespace: biological_process
Definition: The process in which a low-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
Synonyms: LDL clearance
high-density lipoprotein particle clearance (GO:0034384)
Namespace: biological_process
Definition: The process in which a high-density lipoprotein particle is removed from the blood via receptor-mediated endocytosis and its constituent parts degraded.
Synonyms: HDL clearance
triglyceride-rich plasma lipoprotein particle (GO:0034385)
Namespace: cellular_component
Definition: A plasma lipoprotein particle that has a hydrophobic core enriched in triglycerides surrounded by an amphipathic monolayer of phospholipids, cholesterol and apolipoproteins. Triglyceride-rich lipoprotein particles transport lipids, which are non-covalently associated with the particles, in the blood.
Synonyms: triacylglycerol-rich lipoprotein particle; triglyceride-rich lipoprotein particle
4-aminobutyrate:2-oxoglutarate transaminase activity (GO:0034386)
Namespace: molecular_function
Definition: Catalysis of the reaction: 2-oxoglutarate + 4-aminobutanoate = L-glutamate + succinate semialdehyde.
Synonyms: 4-aminobutanoate:2-oxoglutarate aminotransferase activity; 4-aminobutyrate-2-ketoglutarate aminotransferase activity; 4-aminobutyrate-2-oxoglutarate aminotransferase activity; 4-aminobutyrate-2-oxoglutarate transaminase activity; 4-aminobutyric acid 2-ketoglutaric acid aminotransferase activity; GABA-2-oxoglutarate aminotransferase activity; GABA-2-oxoglutarate transaminase activity; GABA-alpha-ketoglutarate aminotransferase activity; GABA-alpha-ketoglutarate transaminase activity; GABA-alpha-ketoglutaric acid transaminase activity; GABA-alpha-oxoglutarate aminotransferase activity; GABA-oxoglutarate aminotransferase activity; GABA-oxoglutarate transaminase activity; gamma-aminobutyrate-alpha-ketoglutarate aminotransferase activity; gamma-aminobutyrate-alpha-ketoglutarate transaminase activity; gamma-aminobutyrate:alpha-oxoglutarate aminotransferase activity; gamma-aminobutyric acid-2-oxoglutarate transaminase activity; gamma-aminobutyric acid-alpha-ketoglutarate transaminase activity; gamma-aminobutyric acid-alpha-ketoglutaric acid aminotransferase activity
4-aminobutyrate:pyruvate transaminase activity (GO:0034387)
Namespace: molecular_function
Definition: Catalysis of the reaction: 4-aminobutanoate + pyruvate = succinate semialdehyde + alanine. Also converts glyoxylate to glycine.
Synonyms: gamma-aminobutyric acid pyruvate transaminase activity
Pwp2p-containing subcomplex of 90S preribosome (GO:0034388)
Namespace: cellular_component
Definition: A protein complex that forms a subcomplex of the 90S preribosome and can interact directly with the 5' External Transcribed Spacer (ETS) of the full length pre-rRNA transcript. In S. cerevisiae, it sediments at 25-30 S and is composed of Pwp2p, Dip2p, Utp21p, Utp13p, Utp18p, and Utp6p.
Synonyms: 25-30 S subcomplex of 90S preribosome; UTP-B complex
Comment: Note that the term name uses Saccharomyces gene product names because no other names have yet arisen for this complex; the term nevertheless can be used for analogous complexes in other eukaryotes, and the name can be changed if better wording is found.
lipid droplet organization (GO:0034389)
Namespace: biological_process
Definition: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lipid particle.
Synonyms: adiposome organization; lipid body organization; lipid particle organisation; lipid particle organization; lipid particle organization and biogenesis
regulation of smooth muscle cell apoptotic process (GO:0034391)
Namespace: biological_process
Definition: Any process that modulates the frequency, rate, or extent of smooth muscle cell apoptotic process.
Synonyms: regulation of SMC apoptosis; regulation of smooth muscle cell apoptosis
negative regulation of smooth muscle cell apoptotic process (GO:0034392)
Namespace: biological_process
Definition: Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process.
Synonyms: down regulation of smooth muscle cell apoptosis; down-regulation of smooth muscle cell apoptosis; downregulation of smooth muscle cell apoptosis; inhibition of smooth muscle cell apoptosis; negative regulation of SMC apoptosis; negative regulation of smooth muscle cell apoptosis
positive regulation of smooth muscle cell apoptotic process (GO:0034393)
Namespace: biological_process
Definition: Any process that activates or increases the frequency, rate, or extent of smooth muscle cell apoptotic process.
Synonyms: activation of smooth muscle cell apoptosis; positive regulation of SMC apoptosis; positive regulation of smooth muscle cell apoptosis; stimulation of smooth muscle cell apoptosis; up regulation of smooth muscle cell apoptosis; up-regulation of smooth muscle cell apoptosis; upregulation of smooth muscle cell apoptosis
protein localization to cell surface (GO:0034394)
Namespace: biological_process
Definition: A process in which a protein is transported to, or maintained in, a location within the external part of the cell wall and/or plasma membrane.
Synonyms: protein localisation at cell surface; protein localization at cell surface
obsolete regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)
Namespace: biological_process
Definition: OBSOLETE. Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter in response to an iron stimulus.
Synonyms: regulation of specific transcription from RNA polymerase II promoter in response to iron
Comment: This term was obsoleted because it represents a GO-CAM model.
obsolete negative regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034396)
Namespace: biological_process
Definition: OBSOLETE. Any process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter in response to an iron stimulus.
Synonyms: down regulation of transcription from RNA polymerase II promoter in response to iron; down-regulation of transcription from RNA polymerase II promoter in response to iron; downregulation of transcription from RNA polymerase II promoter in response to iron; inhibition of transcription from RNA polymerase II promoter in response to iron; negative regulation of transcription from Pol II promoter in response to iron
Comment: This term was obsoleted because it represents a GO-CAM model.
telomere localization (GO:0034397)
Namespace: biological_process
Definition: Any process in which a telomere is transported to, and/or maintained in, a specific location.
Synonyms: telomere localisation
telomere tethering at nuclear periphery (GO:0034398)
Namespace: biological_process
Definition: The process in which a telomere is maintained in a specific location at the nuclear periphery.
nuclear periphery (GO:0034399)
Namespace: cellular_component
Definition: The portion of the nuclear lumen proximal to the inner nuclear membrane.
gerontoplast (GO:0034400)
Namespace: cellular_component
Definition: A plastid found in senescing, formerly green tissues that is derived from a chloroplast that undergoes an organized developmental program of senescence.
obsolete chromatin organization involved in regulation of transcription (GO:0034401)
Namespace: biological_process
Definition: OBSOLETE. Any cellular process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin that modulates the rate, frequency or extent of DNA-dependent transcription.
Synonyms: activation of global transcription from RNA polymerase II promoter by histone modification; activation of transcription from RNA polymerase II promoter by histone modification; establishment or maintenance of chromatin architecture during transcription; positive regulation of gene-specific transcription from RNA polymerase II promoter by histone modification; positive regulation of global transcription from Pol II promoter by histone modification; positive regulation of transcription from Pol II promoter by histone modification; positive regulation of transcription from RNA polymerase II promoter by histone modification; positive regulation of transcription from RNA polymerase II promoter, global by histone modification; regulation of gene-specific transcription from RNA polymerase II promoter by histone modification; regulation of global transcription from Pol II promoter by histone modification; regulation of transcription by chromatin organisation; regulation of transcription by chromatin organization; regulation of transcription from Pol II promoter by histone modification; regulation of transcription from RNA polymerase II promoter by histone modification; regulation of transcription from RNA polymerase II promoter, global by histone modification; stimulation of global transcription from RNA polymerase II promoter by histone modification; stimulation of transcription from RNA polymerase II promoter by histone modification; up regulation of global transcription from RNA polymerase II promoter by histone modification; up regulation of transcription from RNA polymerase II promoter by histone modification; up-regulation of global transcription from RNA polymerase II promoter by histone modification; up-regulation of transcription from RNA polymerase II promoter by histone modification; upregulation of global transcription from RNA polymerase II promoter by histone modification; upregulation of transcription from RNA polymerase II promoter by histone modification
Comment: This term was obsoleted because these it was redundant with other terms: heterochromatin assembly and regulation of gene expression, epigenetic.
obsolete recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex (GO:0034402)
Namespace: biological_process
Definition: OBSOLETE. The process in which proteins required for 3'-end transcript processing become associated with the RNA polymerase II holoenzyme complex and the 3' end of a transcript.
Comment: The reason for obsoletion is that this term represents a molecular function.
alignment of 3' and 5' splice sites of mRNA (GO:0034403)
Namespace: biological_process
Definition: Recognition of both the 5' and 3'-splice sites and positioning them in the correct alignment with respect to each other so that the second catalytic step of nuclear mRNA splicing can occur.
Synonyms: alignment of 3' and 5' splice sites of nuclear mRNA
nucleobase-containing small molecule biosynthetic process (GO:0034404)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
Synonyms: nucleobase, nucleoside and nucleotide anabolism; nucleobase, nucleoside and nucleotide biosynthesis; nucleobase, nucleoside and nucleotide formation; nucleobase, nucleoside and nucleotide synthesis
response to fluid shear stress (GO:0034405)
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 fluid shear stress stimulus. Fluid shear stress is the force acting on an object in a system where the fluid is moving across a solid surface.
cell wall beta-glucan metabolic process (GO:0034406)
Namespace: biological_process
Definition: The chemical reactions and pathways involving beta-glucans, compounds composed of glucose residues linked by beta-D-glucosidic bonds, found in the walls of cells.
Synonyms: cell wall beta-glucan metabolism
cell wall (1->3)-beta-D-glucan metabolic process (GO:0034407)
Namespace: biological_process
Definition: The chemical reactions and pathways involving (1->3)-beta-D-glucans, compounds composed of glucose residues linked by (1->3)-beta-D-glucosidic bonds, found in the walls of cells.
Synonyms: cell wall 1,3-beta-D-glucan metabolic process; cell wall 1,3-beta-glucan metabolic process; cell wall 1,3-beta-glucan metabolism; cell wall beta-1,3 glucan metabolic process; cell wall beta-1,3 glucan metabolism
ascospore wall (1->3)-beta-D-glucan metabolic process (GO:0034409)
Namespace: biological_process
Definition: The chemical reactions and pathways involving (1->3)-beta-D-glucans, compounds composed of glucose residues linked by (1->3)-beta-D-glucosidic bonds, found in the walls of ascospores.
Synonyms: ascospore wall 1,3-beta-D-glucan metabolic process; ascospore wall 1,3-beta-glucan metabolic process; ascospore wall 1,3-beta-glucan metabolism; ascospore wall beta-1,3 glucan metabolic process; ascospore wall beta-1,3 glucan metabolism
cell wall beta-glucan biosynthetic process (GO:0034410)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of beta-glucans, compounds composed of glucose residues linked by beta-D-glucosidic bonds, found in the walls of cells.
Synonyms: cell wall beta-glucan anabolism; cell wall beta-glucan biosynthesis; cell wall beta-glucan formation; cell wall beta-glucan synthesis
ascospore wall beta-glucan biosynthetic process (GO:0034412)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of beta-glucans, compounds composed of glucose residues linked by beta-D-glucosidic bonds, found in the walls of ascospores.
Synonyms: ascospore wall beta-glucan anabolism; ascospore wall beta-glucan biosynthesis; ascospore wall beta-glucan formation; ascospore wall beta-glucan synthesis
ascospore wall (1->3)-beta-D-glucan biosynthetic process (GO:0034413)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of (1->3)-beta-D-glucans, compounds composed of glucose residues linked by (1->3)-beta-D-glucosidic bonds, found in the walls of ascospores.
Synonyms: ascospore wall 1,3-beta-D-glucan biosynthetic process; ascospore wall 1,3-beta-glucan anabolism; ascospore wall 1,3-beta-glucan biosynthesis; ascospore wall 1,3-beta-glucan biosynthetic process; ascospore wall 1,3-beta-glucan formation; ascospore wall 1,3-beta-glucan synthesis; ascospore wall beta-1,3-glucan anabolism; ascospore wall beta-1,3-glucan biosynthesis; ascospore wall beta-1,3-glucan biosynthetic process; ascospore wall beta-1,3-glucan formation; ascospore wall beta-1,3-glucan synthesis
obsolete tRNA 3'-trailer cleavage, exonucleolytic (GO:0034415)
Namespace: biological_process
Definition: OBSOLETE. Exonucleolytic cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA.
Synonyms: exonucleolytic tRNA 3'-end cleavage; exonucleolytic tRNA 3'-trailer cleavage; tRNA 3'-end cleavage, exonucleolytic
Comment: The reason for obsoletion is that the term represents a molecular functions.
obsolete bisphosphoglycerate phosphatase activity (GO:0034416)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: 2,3-diphosphoglycerate + H2O = phosphoglycerate + phosphate.
Synonyms: 2,3-bisphosphoglycerate phosphatase activity; 2,3-diphosphoglycerate phosphatase activity; 2,3-diphosphoglyceric acid phosphatase activity; diphosphoglycerate phosphatase activity; glycerate-2,3-diphosphate phosphatase activity
Comment: This term was obsoleted because it is not different from its child bisphosphoglycerate 3-phosphatase activity ; GO:0034417.
bisphosphoglycerate 3-phosphatase activity (GO:0034417)
Namespace: molecular_function
Definition: Catalysis of the reaction: (2R)-2,3-bisphosphoglycerate + H2O = (2R)-2-phosphoglycerate + phosphate.
Synonyms: 2,3-bisphospho-D-glycerate 3-phosphohydrolase activity
urate biosynthetic process (GO:0034418)
Namespace: biological_process
Definition: The chemical reactions and pathways resulting in the formation of urate, the anion of uric acid, 2,6,8-trioxypurine.
Synonyms: urate anabolism; urate biosynthesis; urate formation; urate synthesis; uric acid biosynthetic process
obsolete L-2-hydroxyglutarate oxidase activity (GO:0034419)
Namespace: molecular_function
Definition: OBSOLETE. Catalysis of the reaction: L-2-hydroxyglutarate + O2 = 2-oxoglutarate + hydrogen peroxide.
Comment: This term was obsoleted because this activity is not believed to exist.
post-translational protein acetylation (GO:0034421)
Namespace: biological_process
Definition: The addition of an acetyl group to one or more amino acids in a protein, occurring after the protein has been completely translated and released from the ribosome.
Synonyms: post-translational protein amino acid acetylation; posttranslational protein amino acid acetylation
aleurone grain lumen (GO:0034422)
Namespace: cellular_component
Definition: The volume enclosed by the membrane of an aleurone grain.
autophagosome lumen (GO:0034423)
Namespace: cellular_component
Definition: The volume enclosed within the autophagosome double-membrane.
Synonyms: autophagic vacuole lumen
Comment: Note that this term should be used for annotating gene products with caution: it should be used only to annotate gene products demonstrated to reside and function normally in the autophagic vacuole lumen, not for molecules that are temporarily found in the lumen prior to degradation.
Vps55/Vps68 complex (GO:0034424)
Namespace: cellular_component
Definition: A membrane-associated protein complex that is required for a late stage of endosomal transport. In budding yeast, this complex consists of Vps55p and Vps68p proteins.
etioplast envelope (GO:0034425)
Namespace: cellular_component
Definition: The double lipid bilayer enclosing the etioplast and separating its contents from the rest of the cytoplasm; includes the intermembrane space.
obsolete nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' (GO:0034427)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction.
Comment: The reason for obsoletion is that this represents an unnecessary grouping term
obsolete nuclear-transcribed mRNA catabolic process, exonucleolytic, 5'-3' (GO:0034428)
Namespace: biological_process
Definition: OBSOLETE. The chemical reactions and pathways resulting in the breakdown of the mRNA transcript body that occurs when the 5' end is not protected by a 5'-cap; degradation proceeds in the 5' to 3' direction.
Comment: The reason for obsoletion is that this term was an unnecessary grouping term.
tectobulbar tract morphogenesis (GO:0034429)
Namespace: biological_process
Definition: Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in the optic tectum towards target cells in the premotor reticulospinal system in the hindbrain.
monolayer-surrounded lipid storage body outer lipid monolayer (GO:0034430)
Namespace: cellular_component
Definition: The single layer of phopholipids surrounding a lipid storage body.
Synonyms: lipid droplet outer lipid monolayer; lipid storage body surface lipid monolayer; oil body outer lipid monolayer; oleosome outer lipid monolayer; spherosome outer lipid monolayer
bis(5'-adenosyl)-hexaphosphatase activity (GO:0034431)
Namespace: molecular_function
Definition: Catalysis of the reaction: P1-P6-bis(5'-adenosyl) hexaphosphate + H2O = AMP + adenosine 5'-pentaphosphate.
Synonyms: AP(6)A hydrolase activity; AP-6-A hydrolase activity; AP6A hydrolase activity; diadenosine 5',5'''-P1,P6-hexaphosphate hydrolase activity
bis(5'-adenosyl)-pentaphosphatase activity (GO:0034432)
Namespace: molecular_function
Definition: Catalysis of the reaction: P1-P6-bis(5'-adenosyl) pentaphosphate + H2O = AMP + adenosine 5'-tetraphosphate.
Synonyms: AP(5)A hydrolase activity; AP-5-A hydrolase activity; AP5A hydrolase activity; Ap5a pyrophosphohydrolase activity; diadenosine 5',5'''-P1,P6-pentaphosphate hydrolase activity
obsolete steroid esterification (GO:0034433)
Namespace: biological_process
Definition: OBSOLETE. A lipid modification process in which a steroid ester is formed by the combination of a carboxylic acid (often a fatty acid) and a steroid molecule (e.g. cholesterol).
Comment: This term was obsoleted because it represents a molecular function.
obsolete sterol esterification (GO:0034434)
Namespace: biological_process
Definition: OBSOLETE. A lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and a sterol molecule (e.g. cholesterol).
Comment: This term was obsoleted because it represents a molecular function.
obsolete cholesterol esterification (GO:0034435)
Namespace: biological_process
Definition: OBSOLETE. A lipid modification process in which a sterol ester is formed by the combination of a carboxylic acid (often a fatty acid) and cholesterol. In the blood this process is associated with the conversion of free cholesterol into cholesteryl ester, which is then sequestered into the core of a lipoprotein particle.
Comment: This term was obsoleted because it represents a molecular function.
glycoprotein transport (GO:0034436)
Namespace: biological_process
Definition: The directed movement of a glycoprotein, a protein that contains covalently bound glycose (i.e. monosaccharide) residues, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
obsolete glycoprotein transmembrane transporter activity (GO:0034437)
Namespace: molecular_function
Definition: OBSOLETE. Enables the transfer of a glycoprotein from one side of a membrane to the other.
Synonyms: glycoprotein transporter activity
Comment: This term was obsoleted because there is no transmembrane transporter specific for glycoproteins.