honicky/genept-composable-embeddings
Updated
description stringlengths 15 3.43k | gene_id stringlengths 2 25 |
|---|---|
Gene Symbol LINC01409 | LINC01409 |
Gene Symbol FAM87B | FAM87B |
Gene Symbol LINC01128 | LINC01128 |
Gene Symbol LINC00115 | LINC00115 |
Gene Symbol FAM41C | FAM41C |
Gene Symbol SAMD11 Predicted to enable several functions, including histone binding activity; protein domain specific binding activity; and protein self-association. Predicted to be involved in negative regulation of transcription, DNA-templated. Predicted to act upstream of or within negative regulation of transcripti... | SAMD11 |
Gene Symbol NOC2L | NOC2L |
Gene Symbol KLHL17 The protein encoded by this gene is expressed in neurons of most regions of the brain. It contains an N-terminal BTB domain, which mediates dimerization of the protein, and a C-terminal Kelch domain, which mediates binding to F-actin. This protein may play a key role in the regulation of actin-based ... | KLHL17 |
Gene Symbol PLEKHN1 Enables phospholipid binding activity. Involved in 3'-UTR-mediated mRNA destabilization; positive regulation of apoptotic process; and response to hypoxia. Located in cytoskeleton and mitochondrial membrane. | PLEKHN1 |
Gene Symbol HES4 Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anterior/posterior pattern specification and regulation of transcription by RNA polymerase II. Predic... | HES4 |
Gene Symbol ISG15 The protein encoded by this gene is a ubiquitin-like protein that is conjugated to intracellular target proteins upon activation by interferon-alpha and interferon-beta. Several functions have been ascribed to the encoded protein, including chemotactic activity towards neutrophils, direction of ligate... | ISG15 |
Gene Symbol AGRN This gene encodes one of several proteins that are critical in the development of the neuromuscular junction (NMJ), as identified in mouse knock-out studies. The encoded protein contains several laminin G, Kazal type serine protease inhibitor, and epidermal growth factor domains. Additional post-transl... | AGRN |
Gene Symbol C1orf159 Predicted to be integral component of membrane. | C1orf159 |
Gene Symbol LINC01342 | LINC01342 |
Gene Symbol TTLL10 Predicted to enable protein-glycine ligase activity, elongating. Predicted to be involved in protein polyglycylation. Predicted to be located in axoneme and microtubule cytoskeleton. | TTLL10 |
Gene Symbol TNFRSF18 This gene encodes a member of the TNF-receptor superfamily. The encoded receptor has been shown to have increased expression upon T-cell activation, and it is thought to play a key role in dominant immunological self-tolerance maintained by CD25(+)CD4(+) regulatory T cells. Knockout studies in mice... | TNFRSF18 |
Gene Symbol TNFRSF4 The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor has been shown to activate NF-kappaB through its interaction with adaptor proteins TRAF2 and TRAF5. Knockout studies in mice suggested that this receptor promotes the expression of apoptosis inhibitors BCL2 a... | TNFRSF4 |
Gene Symbol SDF4 This gene encodes a stromal cell derived factor that is a member of the CREC protein family. The encoded protein contains six EF-hand motifs and calcium-binding motifs. This protein localizes to the Golgi lumen and may be involved in regulating calcium dependent cellular activities. | SDF4 |
Gene Symbol B3GALT6 The enzyme encoded by this intronless gene is a beta-1,3-galactosyltransferase found in the medial Golgi apparatus, where it catalyzes the transfer of galactose from UDP-galactose to substrates containing a terminal beta-linked galactose moiety. The encoded enzyme has a particular affinity for galac... | B3GALT6 |
Gene Symbol C1QTNF12 Predicted to enable hormone activity. Predicted to be involved in negative regulation of gluconeogenesis; positive regulation of glucose import; and positive regulation of insulin receptor signaling pathway. Predicted to act upstream of or within negative regulation of inflammatory response; positi... | C1QTNF12 |
Gene Symbol UBE2J2 The modification of proteins with ubiquitin is an important cellular mechanism for targeting abnormal or short-lived proteins for degradation. Ubiquitination involves at least three classes of enzymes: ubiquitin-activating enzymes, or E1s, ubiquitin-conjugating enzymes, or E2s, and ubiquitin-protein ... | UBE2J2 |
Gene Symbol LINC01786 | LINC01786 |
Gene Symbol SCNN1D Predicted to enable ligand-gated sodium channel activity. Predicted to be involved in sodium ion transmembrane transport. Located in actin cytoskeleton and plasma membrane. | SCNN1D |
Gene Symbol ACAP3 Predicted to enable GTPase activator activity and metal ion binding activity. Predicted to be involved in regulation of catalytic activity. Predicted to act upstream of or within neuron migration and regulation of neuron projection development. Predicted to be located in growth cone. | ACAP3 |
Gene Symbol PUSL1 Predicted to enable pseudouridine synthase activity. Predicted to be involved in tRNA pseudouridine synthesis. Located in mitochondrion. | PUSL1 |
Gene Symbol INTS11 | INTS11 |
Gene Symbol CPTP Enables ceramide 1-phosphate binding activity and ceramide 1-phosphate transfer activity. Involved in several processes, including ceramide 1-phosphate transport; negative regulation of NLRP3 inflammasome complex assembly; and negative regulation of interleukin-1 beta production. Located in cytosol. | CPTP |
Gene Symbol TAS1R3 The protein encoded by this gene is a G-protein coupled receptor involved in taste responses. The encoded protein can form a heterodimeric receptor with TAS1R1 to elicit the umami taste response, or it can bind with TAS1R2 to form a receptor for the sweet taste response. | TAS1R3 |
Gene Symbol DVL1 DVL1, the human homolog of the Drosophila dishevelled gene (dsh) encodes a cytoplasmic phosphoprotein that regulates cell proliferation, acting as a transducer molecule for developmental processes, including segmentation and neuroblast specification. DVL1 is a candidate gene for neuroblastomatous trans... | DVL1 |
Gene Symbol MXRA8 Predicted to be involved in establishment of glial blood-brain barrier. Located in extracellular exosome. | MXRA8 |
Gene Symbol AURKAIP1 Acts upstream of or within positive regulation of proteolysis. Located in mitochondrion and nucleoplasm. | AURKAIP1 |
Gene Symbol CCNL2 The protein encoded by this gene belongs to the cyclin family. Through its interaction with several proteins, such as RNA polymerase II, splicing factors, and cyclin-dependent kinases, this protein functions as a regulator of the pre-mRNA splicing process, as well as in inducing apoptosis by modulatin... | CCNL2 |
Gene Symbol MRPL20-AS1 | MRPL20-AS1 |
Gene Symbol MRPL20 Mammalian mitochondrial ribosomal proteins are encoded by nuclear genes and help in protein synthesis within the mitochondrion. Mitochondrial ribosomes (mitoribosomes) consist of a small 28S subunit and a large 39S subunit. They have an estimated 75% protein to rRNA composition compared to prokaryoti... | MRPL20 |
Gene Symbol ANKRD65 | ANKRD65 |
Gene Symbol VWA1 | VWA1 |
Gene Symbol ATAD3C Predicted to enable zinc ion binding activity. Predicted to be involved in mitochondrion organization. Located in mitochondrion. | ATAD3C |
Gene Symbol ATAD3B The protein encoded by this gene is localized to the mitochondrial inner membrane, where it can bind to a highly-related protein, ATAD3A. ATAD3A appears to interact with matrix nucleoid complexes, and the encoded protein negatively regulates that interaction. This gene is expressed almost exclusively... | ATAD3B |
Gene Symbol ATAD3A This gene encodes a ubiquitously expressed mitochondrial membrane protein that contributes to mitochondrial dynamics, nucleoid organization, protein translation, cell growth, and cholesterol metabolism. This gene is a member of the ATPase family AAA-domain containing 3 gene family which, in humans, i... | ATAD3A |
Gene Symbol TMEM240 This gene encodes a transmembrane-domain containing protein found in the brain and cerebellum. Mutations in this gene result in spinocerebellar ataxia 21. | TMEM240 |
Gene Symbol SSU72 Enables RNA polymerase II CTD heptapeptide repeat phosphatase activity. Involved in dephosphorylation of RNA polymerase II C-terminal domain and mRNA polyadenylation. Located in cytosol and nucleoplasm. | SSU72 |
Gene Symbol FNDC10 Predicted to be integral component of membrane. | FNDC10 |
Gene Symbol MIB2 The protein encoded by this gene is an E3 ubiquitin protein ligase that mediates ubiquitination of proteins in the Notch signaling pathway. The encoded protein may be a suppressor of melanoma invasion. | MIB2 |
Gene Symbol MMP23B This gene (MMP23B) encodes a member of the matrix metalloproteinase (MMP) family, and it is part of a duplicated region of chromosome 1p36.3. Proteins of the matrix metalloproteinase (MMP) family are involved in the breakdown of extracellular matrix in normal physiological processes, such as embryoni... | MMP23B |
Gene Symbol CDK11B This gene encodes a member of the serine/threonine protein kinase family. Members of this kinase family are known to be essential for eukaryotic cell cycle control. Due to a segmental duplication, this gene shares very high sequence identity with a neighboring gene. These two genes are frequently del... | CDK11B |
Gene Symbol SLC35E2B Predicted to enable antiporter activity. Predicted to be involved in transmembrane transport. Predicted to act upstream of or within blastocyst hatching. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. | SLC35E2B |
Gene Symbol CDK11A This gene encodes a member of the serine/threonine protein kinase family. Members of this kinase family are known to be essential for eukaryotic cell cycle control. Due to a segmental duplication, this gene shares very high sequence identity with a neighboring gene. These two genes are frequently del... | CDK11A |
Gene Symbol SLC35E2A Predicted to enable antiporter activity. Predicted to be involved in transmembrane transport. Predicted to be integral component of membrane. Predicted to be active in Golgi apparatus. | SLC35E2A |
Gene Symbol NADK | NADK |
Gene Symbol GNB1 Heterotrimeric guanine nucleotide-binding proteins (G proteins), which integrate signals between receptors and effector proteins, are composed of an alpha, a beta, and a gamma subunit. These subunits are encoded by families of related genes. This gene encodes a beta subunit. Beta subunits are important... | GNB1 |
Gene Symbol CALML6 Predicted to enable calcium ion binding activity and enzyme regulator activity. Predicted to be involved in regulation of catalytic activity. Predicted to be located in cytoplasm and nucleus. | CALML6 |
Gene Symbol TMEM52 Predicted to be integral component of membrane. | TMEM52 |
Gene Symbol CFAP74 Predicted to be involved in axoneme assembly. Predicted to be located in axoneme. | CFAP74 |
Gene Symbol GABRD Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the mammalian brain where it acts at GABA-A receptors, which are ligand-gated chloride channels. Chloride conductance of these channels can be modulated by agents such as benzodiazepines that bind to the GABA-A receptor. The GA... | GABRD |
Gene Symbol PRKCZ Protein kinase C (PKC) zeta is a member of the PKC family of serine/threonine kinases which are involved in a variety of cellular processes such as proliferation, differentiation and secretion. Unlike the classical PKC isoenzymes which are calcium-dependent, PKC zeta exhibits a kinase activity which i... | PRKCZ |
Gene Symbol PRKCZ-AS1 | PRKCZ-AS1 |
Gene Symbol FAAP20 Enables K63-linked polyubiquitin modification-dependent protein binding activity and ubiquitin-dependent protein binding activity. Involved in interstrand cross-link repair and translesion synthesis. Located in cell junction; chromosome; and nuclear body. Part of Fanconi anaemia nuclear complex. | FAAP20 |
Gene Symbol SKI This gene encodes the nuclear protooncogene protein homolog of avian sarcoma viral (v-ski) oncogene. It functions as a repressor of TGF-beta signaling, and may play a role in neural tube development and muscle differentiation. | SKI |
Gene Symbol MORN1 | MORN1 |
Gene Symbol RER1 The protein encoded by this gene is a multi-pass membrane protein that is localized to the golgi apparatus. It is involved in the retention of endoplasmic reticulum (ER) membrane proteins in the ER and retrieval of ER membrane proteins from the early Golgi compartment to facilitate gamma-secretase comp... | RER1 |
Gene Symbol PEX10 This gene encodes a protein involved in import of peroxisomal matrix proteins. This protein localizes to the peroxisomal membrane. Mutations in this gene result in phenotypes within the Zellweger spectrum of peroxisomal biogenesis disorders, ranging from neonatal adrenoleukodystrophy to Zellweger synd... | PEX10 |
Gene Symbol PLCH2 | PLCH2 |
Gene Symbol PANK4 This gene encodes a protein belonging to the pantothenate kinase family. Pantothenate kinase is a key regulatory enzyme in the biosynthesis of coenzyme A (CoA) in bacteria and mammalian cells. It catalyzes the first committed step in the universal biosynthetic pathway leading to CoA and is itself subj... | PANK4 |
Gene Symbol TNFRSF14-AS1 | TNFRSF14-AS1 |
Gene Symbol TNFRSF14 This gene encodes a member of the TNF (tumor necrosis factor) receptor superfamily. The encoded protein functions in signal transduction pathways that activate inflammatory and inhibitory T-cell immune response. It binds herpes simplex virus (HSV) viral envelope glycoprotein D (gD), mediating its e... | TNFRSF14 |
Gene Symbol PRXL2B Predicted to enable antioxidant activity and prostaglandin-F synthase activity. Predicted to be involved in prostaglandin biosynthetic process. Located in extracellular exosome. | PRXL2B |
Gene Symbol MMEL1 The protein encoded by this gene is a member of the neutral endopeptidase (NEP) or membrane metallo-endopeptidase (MME) family. Family members play important roles in pain perception, arterial pressure regulation, phosphate metabolism and homeostasis. This protein is a type II transmembrane protein an... | MMEL1 |
Gene Symbol TTC34 | TTC34 |
Gene Symbol PRDM16 The reciprocal translocation t(1;3)(p36;q21) occurs in a subset of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). This gene is located near the 1p36.3 breakpoint and has been shown to be specifically expressed in the t(1:3)(p36,q21)-positive MDS/AML. The protein encoded by this gene... | PRDM16 |
Gene Symbol MEGF6 Predicted to enable calcium ion binding activity. Predicted to be located in extracellular region. | MEGF6 |
Gene Symbol TPRG1L Predicted to enable identical protein binding activity. Predicted to be involved in regulation of glutamatergic synaptic transmission. Located in extracellular exosome. | TPRG1L |
Gene Symbol WRAP73 This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in... | WRAP73 |
Gene Symbol TP73 This gene encodes a member of the p53 family of transcription factors involved in cellular responses to stress and development. It maps to a region on chromosome 1p36 that is frequently deleted in neuroblastoma and other tumors, and thought to contain multiple tumor suppressor genes. The demonstration ... | TP73 |
Gene Symbol CCDC27 | CCDC27 |
Gene Symbol SMIM1 This gene encodes a small, conserved protein that participates in red blood cell formation. The encoded protein is localized to the cell membrane and is the antigen for the Vel blood group. Alternative splicing results in different transcript variants that encode the same protein. | SMIM1 |
Gene Symbol LRRC47 Enables RNA binding activity. Predicted to be involved in phenylalanyl-tRNA aminoacylation. | LRRC47 |
Gene Symbol CEP104 This gene encodes a centrosomal protein required for ciliogenesis and for ciliary tip structural integrity. The mammalian protein contains three amino-terminal hydrophobic domains, two glycosylation sites, four cysteine-rich motifs, and two regions with homology to the glutamate receptor ionotropic, ... | CEP104 |
Gene Symbol DFFB Apoptosis is a cell death process that removes toxic and/or useless cells during mammalian development. The apoptotic process is accompanied by shrinkage and fragmentation of the cells and nuclei and degradation of the chromosomal DNA into nucleosomal units. DNA fragmentation factor (DFF) is a heterodi... | DFFB |
Gene Symbol C1orf174 Located in nucleoplasm. | C1orf174 |
Gene Symbol LINC01134 | LINC01134 |
Gene Symbol LINC02780 | LINC02780 |
Gene Symbol AJAP1 Enables beta-catenin binding activity. Involved in negative regulation of cell-matrix adhesion; negative regulation of wound healing; and regulation of polarized epithelial cell differentiation. Located in several cellular components, including adherens junction; basolateral plasma membrane; and cell-... | AJAP1 |
Gene Symbol NPHP4 This gene encodes a protein involved in renal tubular development and function. This protein interacts with nephrocystin, and belongs to a multifunctional complex that is localized to actin- and microtubule-based structures. Mutations in this gene are associated with nephronophthisis type 4, a renal d... | NPHP4 |
Gene Symbol KCNAB2 Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte trans... | KCNAB2 |
Gene Symbol CHD5 This gene encodes a member of the chromodomain helicase DNA-binding protein family. Members of this family are characterized by a chromodomain, a helicase ATP-binding domain and an additional functional domain. This gene encodes a neuron-specific protein that may function in chromatin remodeling and ge... | CHD5 |
Gene Symbol RPL22 Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a cytoplasmic ribosomal protein that is a component of the 60S... | RPL22 |
Gene Symbol RNF207 Enables Hsp70 protein binding activity; chaperone binding activity; and transmembrane transporter binding activity. Involved in positive regulation of delayed rectifier potassium channel activity; positive regulation of gene expression; and positive regulation of voltage-gated potassium channel activ... | RNF207 |
Gene Symbol ICMT This gene encodes the third of three enzymes that posttranslationally modify isoprenylated C-terminal cysteine residues in certain proteins and target those proteins to the cell membrane. This enzyme localizes to the endoplasmic reticulum. Alternative splicing may result in other transcript variants, b... | ICMT |
Gene Symbol GPR153 This gene encodes an integral membrane protein that belongs to the Class A rhodopsin superfamily of G protein coupled receptors. The encoded protein is expressed primarily in the central nervous system. A knockdown of the orthologous gene in rat is associated with a significant reduction in food inta... | GPR153 |
Gene Symbol ACOT7 This gene encodes a member of the acyl coenzyme family. The encoded protein hydrolyzes the CoA thioester of palmitoyl-CoA and other long-chain fatty acids. Decreased expression of this gene may be associated with mesial temporal lobe epilepsy. Alternatively spliced transcript variants encoding distinc... | ACOT7 |
Gene Symbol HES2 Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in anterior/posterior pattern specification; regulation of neurogenesis; and regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleus. | HES2 |
Gene Symbol ESPN This gene encodes a multifunctional actin-bundling protein. It plays a major role in regulating the organization, dimensions, dynamics, and signaling capacities of the actin filament-rich, microvillus-type specializations that mediate sensory transduction in various mechanosensory and chemosensory cell... | ESPN |
Gene Symbol TNFRSF25 The protein encoded by this gene is a member of the TNF-receptor superfamily. This receptor is expressed preferentially in the tissues enriched in lymphocytes, and it may play a role in regulating lymphocyte homeostasis. This receptor has been shown to stimulate NF-kappa B activity and regulate cel... | TNFRSF25 |
Gene Symbol PLEKHG5 This gene encodes a protein that activates the nuclear factor kappa B (NFKB1) signaling pathway. Mutations in this gene are associated with autosomal recessive distal spinal muscular atrophy. Multiple transcript variants encoding different isoforms have been found for this gene. | PLEKHG5 |
Gene Symbol NOL9 Enables polynucleotide 5'-hydroxyl-kinase activity. Involved in maturation of 5.8S rRNA. Located in intermediate filament cytoskeleton and nucleolus. | NOL9 |
Gene Symbol TAS1R1 The protein encoded by this gene is a G protein-coupled receptor and is a component of the heterodimeric amino acid taste receptor T1R1+3. The T1R1+3 receptor responds to L-amino acids but not to D-enantiomers or other compounds. Most amino acids that are perceived as sweet activate T1R1+3, and this ... | TAS1R1 |
Gene Symbol ZBTB48 Enables double-stranded telomeric DNA binding activity; identical protein binding activity; and transcription cis-regulatory region binding activity. Involved in positive regulation of transcription, DNA-templated and telomere maintenance via telomere lengthening. Located in chromosome, telomeric reg... | ZBTB48 |
Gene Symbol KLHL21 Enables cullin family protein binding activity. Contributes to ubiquitin-protein transferase activity. Involved in chromosome passenger complex localization to spindle midzone; protein ubiquitination; and regulation of cytokinesis. Located in polar microtubule. Part of Cul3-RING ubiquitin ligase comp... | KLHL21 |
Gene Symbol PHF13 Enables chromatin binding activity. Involved in mitotic chromosome condensation. Located in nucleus. | PHF13 |
Gene Symbol THAP3 Predicted to enable DNA binding activity and metal ion binding activity. Involved in positive regulation of transcription by RNA polymerase II. | THAP3 |
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Gene Description Dataset
This dataset reproduces and expands upon the GenePT project and paper, and makes it easier to reproce and access using standard tools. The goal is to allow users to compose embeddings across dimensions in order to specialize for specific tasks, and add to the existing base embeddings by generating new descriptions and embedding them in the same space.
Dataset Description
This dataset
- reproduces the data from the GenePT project and paper in a more easy-to-use format. This paper itself aggregates data from multiple sources, so please refer to the paper and repository for detailed source information. Citation: Chen YT, Zou J. (2023+) GenePT: A Simple But Effective Foundation Model for Genes and Cells Built From ChatGPT. bioRxiv preprint: https://www.biorxiv.org/content/10.1101/2023.10.16.562533v2. GitHub: https://github.com/yiqunchen/GenePT
- Adds descriptions of genes extracted from various LLMs, across multiple dimensions, such as regulatory pathways, drug interactions, etc. Currently we use GPT-4o-mini to generate descriptions, and only have a combined description that includes several factors. We will add composable dimensions soon
Dataset Structure
The dataset contains six sub-datasets:
- NCBI Summary - Contains gene descriptions from NCBI
- NCBI-UniProt Summary - Contains combined gene descriptions from NCBI and UniProt
- Gene Info Table - Contains contains a mapping between gene_id, ensmble_id and gene functional annotation
- Generated Descriptions (Aging)
- Contains AI-generated gene descriptions
- Model: GPT-4o-mini
- Factors: a. Associated genes b. Aging related information c. Drug interactions d. Pathways and biological processes
- Generated Descriptions (Cell Type and other)
- Contains AI-generated gene descriptions
- Model: GPT-4o-mini
- Factors: a. Associated genes b. Cell type c. Drug interactions d. Pathways and biological processes
- Generated Descriptions (Cell Type only, gpt4o)
- Contains AI-generated gene descriptions
- Model: GPT-4o
- Factors: a. Cell type
- Generated Descriptions (Cell Type and others, gpt4o)
- Contains AI-generated gene descriptions
- Model: GPT-4o
- Factors: a. Cell type b. Tissue type c. Drugs d, Pathways and biological processes
Source Data:
Some of the data was sourced from the following sources upstream of the GenePT project:
- NCBI Gene Database
- UniProt Database The licenses for these databases continue to apply where applicable.
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