Korean, Edit

Gene Library 

Recommendation: 【Bioinformatics】 Bioinformatics Index


1. Overview

2. Description of each gene


a. Gene Score Library 

b. Cell Type Marker Genes



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.

Homo sapiens (human)

① Genes are all capital letters.

36601 genes based on GRCh38 reference (ENSG)

Human gene annotation (24424 genes)

○ Gene ID

○ Entrez ID

○ chromosome number, start, end, width

○ strand

○ transcript ID (transcript_id)

○ bioType

○ aliases

○ protein ID (p_id)

○ description

Mus musculus (mouse)

① Only the first letter of the gene is uppercase and the rest is lowercase

32285 genes based on mm10 reference (ENSMUSG)

Gene homology between human and mouse

Mouse gene annotation (23282 genes)

○ 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

○ Afp: Encoding the fetal serum proteinEalfa feto-protein

○ ALOX5A: Synthesis of LXA4, an anti-inflammatory lipoxin

○ ALOX5AP: Synthesis of LXA4, an anti-inflammatory lipoxin

○ 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

○ 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

○ 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

○ CD74: 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

○ 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

○ DMMT1

○ A transcription factor involved in epigenetic regulation of promoter DNA

○ ELOVL

○ Promote the elongation of fatty acid carbon chain.

○ ENG: Immunomodulation-related gene 

○ 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

○ 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.

○ Gad2: Late maturation marker

○ GATA4: a known congenital heart disease gene.

○ GDF15: T cell inhibitor

○ GFAP: Expression in brain white matter

○ 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

○ 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

○ INSR: Insulin response

○ IRF7: 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

○ 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

○ 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

○ 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

○ PDPN: podoplanin

○ 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

○ 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

○ Sfrp1: Wnt signaling modulator

○ Six6: A key gene involved in eye development

○ Slc17a6/7/8: glutamate neurotransmitter transporter

○ Slc32a1: GABA neurotransmitter transporter

○ SLC46A3

○ A lysosomal transporter

Negative regulator for lipid-based nanoparticle uptake

○ 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

○ 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.

○ 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

○ 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.

○ 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

○ 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

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