Gene Library
Recommendation: 【Bioinformatics】 Bioinformatics Index
1. Overview
1. Overview
⑴ Notation rule
① When referring to genes, italics (e.g., COL1A1) are used, and when referring to proteins, vertical characters (e.g., COL1A1) are used.
② However, here, I will unify them by vertical characters.
⑵ Homo sapiens (human)
① Genes are all capital letters.
○ Gene ID
○ Entrez ID
○ chromosome number, start, end, width
○ strand
○ transcript ID (transcript_id)
○ bioType
○ aliases
○ protein ID (p_id)
○ description
⑶ Mus musculus (mouse)
① Only the first letter of the gene is uppercase and the rest is lowercase
○ Gene ID
○ Entrez ID
○ chromosome number, start, end, width
○ strand
○ protein ID (p_id)
○ transcript ID (transcript_id)
○ tss_id
○ bioType
○ Aliases
○ Description
⑷ For other information, see https://www.scinapse.io/, https://typeset.io/, which curated billions of papers.
2. Description of each gene
○ ABCA1: It plays a role in cholesterol transport
○ ABCC11
○ Related to body odor
○ Type 1. Type A gene: Less apocrine sweat, resulting in weaker body odor
○ Type 2. Type G gene: Active secretion of sweat from apocrine glands
○ Type 3. Type AA gene: There is also a Type AA gene that does not mix with the Type G gene
○ The Type A gene is common in East Asians, while the Type G gene is more frequently expressed in Africans and Europeans
○ In relation to the expression of the ABCC11 gene, Koreans are among the ethnic groups with the least body odor.
○ Additional Explanation on Aging and Body Odor: As we age, the amount of a substance called nonenal, which is produced when fatty acids in sebum oxidize, increases. This substance accumulates in the pores, creating a musty odor. Additionally, after the age of 40, the ability to eliminate nonenal gradually decreases due to a decrease in beneficial skin bacteria, skin acidification, and changes in lipid composition, resulting in stronger body odor.
○ ACKR3
○ Upregulation may occur in activated endothelial cells
○ It may contribute to tumor angiogenesis
○ ACTA2, Acta2 (α-SMA)
○ structural marker
○ smooth muscle actin gene
○ ActB, ACTB: Related to actin. cell motility
○ ACTG2: Related to cell motility
○ ADAM8
○ Encoding disintegrin and metalloprotease domain
○ Membrane-anchored protein
○ ADARB1: Encoding A-to-I (adenosine-to-inosine) RNA editing enzyme
○ Afp: Encoding the fetal serum proteinEalfa feto-protein
○ ALOX5A: Synthesis of LXA4, an anti-inflammatory lipoxin
○ ALOX5AP: Synthesis of LXA4, an anti-inflammatory lipoxin
○ ANCR: Suppression of epidermal differentiation
○ ANXA1: Repressor of inflammation in T cells
○ AQP1: Aquaporin gene, alveolar endothelial cell marker
○ AREG: Related to fibrosis by TGF-β
○ ARHGAP11B: A gene that only humans have. A gene that makes human smart
○ ATP2B2: Autism and schizophrenia show a strong missense mutation signal.
○ BCL11B: Expressed in T cell as a gene that makes B cell lymphoma
○ BRCA1: The loss of function for BRCA1 is associated with tandem duplications.
○ BRCA2: The loss of function for BRCA2 is associated with chromosomal deletions.
○ C1Qb: Modulates synapse elimination
○ C3: It suppresses the infiltration and function of CD8+ and CD4+ T cells.
○ C5ar1: Related to innate immunity
○ CAIX: hypoxia marker
○ CALCRL: a marker of stemness
○ CCL2: Chemokine that induces immune cells such as macrophages and T cells
○ CCL18: Associated with breast cancer metastasis
○ CCL19: Related to inflammatory reactions associated with allergies
○ CCR9: Mediates T lymphocyte development and migration
○ Cd6: Related to immune cell activation
○ CD24: T cell survival
○ CD29: integrin β-1
○ CD31 (PECAM-1; platelet/endothelial cell adhesion molecule-1)
○ Characteristic: 130-kDa glycoprotein, transmembrane protein
○ One of the immunoglobulin superfamily genes
○ Expressed in endothelial cells, platelets, white blood cells, etc
○ Function 1. Engaged in cell-cell interaction: White blood cells-endothelial cells or endothelial cells-endothelial cells
○ Function 2. Activate integrin in white blood cells → activate inflammatory response
○ Function 3. Angiogenesis and vascular stabilization
○ CD46: Limits complement function
○ CD55: Limits complement function
○ CD58: Related to lymphocyte adhesion
○ CD69: An early activation marker of T cell
○ CD74: Pro-inflammatory. A known marker for metastatic tumor growth in breast cancer
○ CD80: T cell co-stimulation
○ CD163: Scavenger receptor
○ CD276
○ Encodes an immune checkpoint receptor, B7-H3, which is involved in T-cell regulation
○ overexpressed on tumor vasculature
○ a target of ongoing cancer immunotherapy clinical trials in solid tumors
○ CD320: Immunoglobulin
○ CD44
○ A known marker of breast cancer stem-like cells and stabilizes Treg persistence
○ CDC7: CDC7 inhibition delays or prevents escape from targeted therapy.
○ Cdkn1a: cell cycle inhibitor
○ Cdh17
○ Encoding a cadherin protein
○ Cadherin protein is associated with activation of Wnt signaling
○ CHIT: Encodes chitotriosidase
○ CLIC6: A key gene upregulated in IPF
○ CLU
○ Encodes clusterin: 75-80 kDa. Heterodimer proteins linked by disulfide bonds
○ Related to cell debris removal and apoptosis inhibition
○ COL1A1: Type I collagen
○ Extracellular matrix.
○ One of the activated fibroblast markers.
○ Both normal fibroblasts and cancerous fibroblasts express COL1A1.
○ It facilitates tumor growth inhibition by activating fibroblasts.
○ COL1A2: Type I collagen
○ Extracellular matrix.
○ One of the activated fibroblast markers.
○ Normal fibroblasts express COL1A2, while in cancerous fibroblasts, expression of COL1A2 is inhibited by methylation.
○ It facilitates tumor growth inhibition by activating fibroblasts.
○ Col3a1: Associated with poor prognosis in colorectal cancer.
○ Col4a1: Related to collagen synthesis
○ Col4a2: Related to collagen synthesis
○ Col6a3 (type VI collagen alpha3): Biomarker of hepatic fibrosis
○ Col7a1: Related to collagen synthesis
○ Col12a1: Related to collagen synthesis
○ COL22A1
○ Encodes collagen type XXII α1 chain
○ Expressed in muscle-tendon junctions at skeletal muscle or cardiac muscle
○ CSF1
○ Encodes a cytokine important for the activation and differentiation of myeloid cells
○ GM-CSF(granulocyte-macrophage colony-stimulating factor)
○ The beta chain of the GM-CSF receptor is not expressed in most resting T cells: This is to prevent over-reaction.
○ Higher expression of GM-CSF than normal levels is required for activation of the alpha chain of the GM-CSF receptor.
○ Cst7: A biomarker of inflammation with the amyloid beta plaque in Alzheimer’s disease.
○ CTHRC1: pathological, pulmonary fibrosis-associated fibroblast marker
○ CXCL8: neutrophil chemoattractant
○ CXCL12
○ Secreted by CAFs and other stromal cells.
○ Case 1. Autocrine fashion → Desmoplasia activation
○ Case 2. Paracrine fashion → Immune cell chemotaxis modulation
○ CXCL13: B cell chemoattractant, immune cell homing
○ Cyp2e1: central lobule marker in liver
○ DCN
○ Expressed in fibroblast
○ Combined with Type I collagen and Type II collagen to the basal membrane
○ Dlx2: Transcription factor Dlx2 determines GABAergic differentiation of neuronal precursors.
○ DMMT1
○ A transcription factor involved in epigenetic regulation of promoter DNA
○ ELOVL
○ Promote the elongation of fatty acid carbon chain.
○ ENG: Immunomodulation-related gene
○ FASN: A biomarker for invasive cancer cell
○ FGF2
○ A protumor angiogenesis factor and induces drug resistance in chemotherapy in breast cancer
○ FGFR1
○ Induces the recruitment of macrophages and MDSCs in the tumor
○ FGFR2
○ FGF7 and FGF10 activate FGFR2b, while not for FGFR2c. (ref)
○ FOLH1
○ Endoces PSMA(prostate-specific membrane antigen)
○ Antigens isolated from the cancel cell line
○ Originally, if the tumor grade is high, it is common to have neotigen and express it less, but the higher the tumor grade, the more it is expressed
○ PSA is identified in serum but PSMA is expressed in membrane and not in serum
○ anti-PSMA antibody: J591
○ Standard treatment for prostate cancer is changing to PSMA targeting radiation drugs
○ FOXA1: A pioneer transcription factor required for breast and prostate cancer cells.
○ Gad1: A glutamate decarboxylase involved in synthesizing the inhibitory neurotransmitter GABA
○ Gad2: Late maturation marker
○ GATA4: a known congenital heart disease gene.
○ GDF15: T cell inhibitor
○ GFAP: Expression in brain white matter. Gliosis marker
○ GLI2
○ A major Hedgehog pathway regulator.
○ It is expressed in fibroblasts.
○ It forms niche-supportive hormone-responsive signaling via enhancing production of growth factors IGF, WNT, FGF, and HGF.
○ GLS: Can metabolize glutamine to glutamate
○ GLUL
○ Central lobule marker in liver
○ Catalyzes the metabolism of glutamate to glutamine
○ Gm42418
○ Expressed a lot at a necrotic region in solid tumor
○ GPR15: T cell trafficking
○ GZMA (granzyme A): Constitutes CYT(cytolytic activity score)
○ GZMK: Associated with immune system dysfunction in inflammatory response
○ HAVCR2: Encodes an immune checkpoint receptor, TIM-3
○ [HBB](https://nate9389.tistory.com/2209#:~:text=%E2%91%A1-,HBB,-(hemoglobin%20subunit%20beta)
○ Hemoglobin gene
○ One of the most efficient mammalian mRNAs
○ Actively utilized in mRNA translation and stability test
○ HCN1: Encodes a major pore forming subunit of HCN channels
○ HLA: Related to human immunity
○ HOXB13: Prostate lineage marker
○ Icam1: Related to immune cell recruitment
○ IGFBP: Insulin response
○ IGFBP2: A biomarker of idiopathic pulmonary fibrosis(IPF)
○ IGHA: IgA
○ IGHG: IgG
○ Il10ra: Related to immune cell recruitment
○ IL6ST: Interleukin-6 signaling
○ INSR: Insulin response
○ IRF7: canonical type 1 interferon marker. Promotes metastasis
○ Itgal: Related to immune cell recruitment
○ JAZF1
○ Encodes juxtaposed with another zinc finger protein 1
○ Involved in lipid metabolism, sugar metabolism, insulin sensitivity, etc
○ KLK3
Encodes PSA(protate-specific antigen)
Found in serum unlike PSMA
○ KLRC2: T cell lectin
○ LAG3: Immune checkpoint marker
○ LCN (lipocalin-1)
○ There are 19 types of LCN-like genes in the human genome
○ There are 45 LCN-like genes in the mouse genome
○ It is found a lot in the necrotic region of solid tumor
○ Lmod3: Related to nemaline myopathy
○ Lrat: Encoding lecithin retinol acyltransferase
○ MALAT1
○ lncRNA MALAT1 is one of the most nucleus-enriched genes.
○ It affects the regulatory function of T cells
○ Mif
○ A secreted ligand.
○ It plays a pleiotropic role in immunity and inflammation modulation to aid in tumor immune evasion.
○ It limits macrophage movement within tissue.
○ MKI67: Proliferation marker. Encodes Ki-67
○ Mmp3: Related to ECM decomposition
○ MMP7: Pulmonary fibrosis marker
○ MOBP: Expressed a lot in brain white matter. A marker gene for oligodendrocyte.
○ Msx1
○ Homeobox gene
○ Encodoes transcription factors associated with WNT5A
○ Ncf4: Related to immune cell activation.
○ NDRG1: Associated with hypoxia.
○ NKX2-1: A mutation in this gene was observed in brain-lung-thyroid syndrome
○ NR4A1: A key mediator of T cell dysfunction
○ Nrxn2: Encodes Neurexin 2, a key gene in the vertebrate nervous system
○ NSF: Involved in the fusion of vesicles with cellular organelles.
○ ODC1: Catalyzes the first step of polyamine biosynthesis.
○ PCNA: Cell proliferation marker
○ PDCD1: Encodes an immune checkpoint receptor, PD-1
○ Pdgfra: It is essential for oligodendrocyte differentiation
○ PDPN: podoplanin. pEMT marker
○ PIK3AP1: Encodes a Toll-like receptor (TLR) signaling adapter crucial for linking TLRs to phosphoinositide-3-kinase (PI3K) activation.
○ Plcg2: Related to immune cell activation
○ Plvap
○ mediates microvascular permeability
○ required for the formation of caveolae and transendothelial channels
○ also increased in tumor vasculature
○ PRELP
○ Expressed in fibroblast
○ Encodes prolargin, an extracellular matrix protein
○ Combined with Type I collagen and Type II collagen to the basal membrane
○ PRF1 (perforin-1): Constitutes CYT(cytolytic activity score)
○ PRSS23: A serine protease associated with proliferation of breast cancer cells
○ PRSS56: hyperopia at the loss-of-function, and myopia at the gain-of-function.
○ Psmb8: Related antigen presenting
○ RARRES2: T cell chemokine
○ Rbp1: Retinol binding protein
○ RORC: Encodes RORγt
○ RPL18: Activate protein translation by [mTOR](https://nate9389.tistory.com/1424#:~:text=%E2%91%B8%20%EC%A2%85%EB%A5%98%204.-,mTOR,-(mammalian%20target%20of)
○ S100A4, S100a4
○ Related to innate immunity
○ Hypoxia-inducible gene promoted by HIF-1
○ Related to cancer metastasis by promoting angiogenesis of tumor
○ S100A8 (MRP8)
○ Consists of 93 amino acids
○ Bind well to divalent cations such as calcium and zinc
○ The name S100 is attached because it dissolves 100% in saturated ammonium sulfate
○ Associated with intrinsic immunity: released from neutrophils, mononucleocytes, and macrophages
○ 45% of neutrophil cytoplasmic protein
○ Monocytes-derived cells continue to secrete S100A8 at low levels
○ Helix-loop-helix structure
○ S100A8 homodimer is unstable and exists as S100A8/S100A9 heterodimer
○ Known as the inflammatory response marker gene
○ Found a lot in the necrotic region of solid tumor
○ S100A9 (MRP14)
○ Consists of 113 amino acids
○ Bind well to divalent cations such as calcium and zinc
○ The name S100 is attached because it dissolves 100% in saturated ammonium sulfate
○ Associated with intrinsic immunity: released from neutrophils, mononucleocytes, and macrophages
○ 45% of neutrophil cytoplasmic protein
○ Monocytes-derived cells continue to secrete S100A9 at low levels
○ Helix-loop-helix structure
○ Known as the inflammatory response marker gene
○ Found a lot in the necrotic region of solid tumor
○ SDS: Portal lobular marker in liver
○ SELENBP1: selenium transporter
○ Sell: Related to innate immunity
○ Sema7a: Involved in differentiation and signaling within endothelial cells.
○ Serpini1: Axon growth
○ Sfrp1: Wnt signaling modulator
○ Six6: A key gene involved in eye development
○ Slc1a2: Glutamate transporter
○ Slc17a6/7/8: glutamate neurotransmitter transporter
○ Slc25a4: ion exchange
○ Slc32a1: GABA neurotransmitter transporter
○ SLC46A3
○ A lysosomal transporter
○ Smad6: Plays a crucial role in maintaining the barrier function of endothelial cells
○ Sox2: Involved in the development of nervous tissue and optic nerve formation
○ SPI1: A regulator of the NCF2 gene
○ SPIC: Modulates myeloid-lineage genes
○ Spp1
○ Encoding osteopontin
○ Pro-angiogenesis
○ Expressed in invasive macrophage, and these macrophages are mostly pro-tumor TAMs.
○ SPRY1 : MAPK regulator
○ SRRM2
○ A component of spliceosomes
○ SRRM2 protein is a key marker of nuclear speckles (NS).
○ It organizes NS formation via liquid condensation.
○ Syt1: vesicle trafficking
○ TAGLN: Tumor suppressor
○ Tap1: Related to antigen presenting
○ Tap2: Related to antigen presenting
○ TBX5: a congenital heart disease gene
○ TCF7: a gene encoding TCF-1. Progenitor Tex cells
○ TDP-43: Unlike in healthy individuals, in ALS, the TDP-43 protein moves from the nucleus to the cytoplasm.
○ TEAD4: A transcription factor involved in the Hippo signalling pathway
○ TGFB2 (TGF-β2): Activates TGFβRⅢ, so it induces the expression of p38 MAPK resulting in dormancy
○ TGM1: differentiation marker transglutaminase 1
○ THRA1/BTR: The only human gene name that contains a ‘/’
○ THY1 (Thy-1): Promotes the generation of antibodies
○ TIM-3
○ The TIM-3 receptor has galectin-9 as its ligand.
○ There are two types: a membrane-bound form and a soluble form.
○ TINCR: Epidermal terminal differentiation (protein-binding RNA)
○ TMBIM6: It plays a role in the progression of cancers through mTORC2 and AKT activation.
○ TOX: A gene encoding a crucial TF of T cell exhaustion
○ TRIM2: Relevant for regulating pulmonary fibrosis
○ TRIM8: An E3 ubiquitin ligase
○ TSC2: It encodes a negative regulator of mTOR
○ TTN: Titin is the longest known human protein at ~34,000 amino acids.
○ Tubb2b: Tubulin beta-2B chain
○ WNT5A, Wnt5a
○ Encodes cytokine related to Wnt signaling pathway
○ The mutation in this gene causes Robinow syndrome
Input: 2022.06.02 20:52