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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for AGPAT2 |
Basic gene info. | Gene symbol | AGPAT2 |
Gene name | 1-acylglycerol-3-phosphate O-acyltransferase 2 | |
Synonyms | 1-AGPAT2|BSCL|BSCL1|LPAAB|LPAAT-beta | |
Cytomap | UCSC genome browser: 9q34.3 | |
Genomic location | chr9 :139567594-139581911 | |
Type of gene | protein-coding | |
RefGenes | NM_001012727.1, NM_006412.3, | |
Ensembl id | ENSG00000169692 | |
Description | 1-AGP acyltransferase 21-AGPAT 21-acyl-sn-glycerol-3-phosphate acyltransferase beta1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)lysophosphatidic acid acyltransferase betalysophosphatidic acid acyltransfe | |
Modification date | 20141219 | |
dbXrefs | MIM : 603100 | |
HGNC : HGNC | ||
Ensembl : ENSG00000169692 | ||
HPRD : 04373 | ||
Vega : OTTHUMG00000020936 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_AGPAT2 | |
BioGPS: 10555 | ||
Gene Expression Atlas: ENSG00000169692 | ||
The Human Protein Atlas: ENSG00000169692 | ||
Pathway | NCI Pathway Interaction Database: AGPAT2 | |
KEGG: AGPAT2 | ||
REACTOME: AGPAT2 | ||
ConsensusPathDB | ||
Pathway Commons: AGPAT2 | ||
Metabolism | MetaCyc: AGPAT2 | |
HUMANCyc: AGPAT2 | ||
Regulation | Ensembl's Regulation: ENSG00000169692 | |
miRBase: chr9 :139,567,594-139,581,911 | ||
TargetScan: NM_001012727 | ||
cisRED: ENSG00000169692 | ||
Context | iHOP: AGPAT2 | |
cancer metabolism search in PubMed: AGPAT2 | ||
UCL Cancer Institute: AGPAT2 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for AGPAT2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: AGPAT2 |
Familial Cancer Database: AGPAT2 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
Metabolic Pathway Description | |
KEGG_GLYCEROLIPID_METABOLISM KEGG_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: AGPAT2 |
MedGen: AGPAT2 (Human Medical Genetics with Condition) | |
ClinVar: AGPAT2 | |
Phenotype | MGI: AGPAT2 (International Mouse Phenotyping Consortium) |
PhenomicDB: AGPAT2 |
Mutations for AGPAT2 |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows AGPAT2 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=11) | (# total SNVs=6) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 10 SNVs Having the Most Samples in COSMIC data |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr9:139568309-139568309 | p.L244L | 2 |
chr9:139571064-139571064 | p.G187G | 2 |
chr9:139571443-139571443 | p.A154A | 1 |
chr9:139571923-139571923 | p.R90C | 1 |
chr9:139571488-139571488 | p.F139L | 1 |
chr9:139571924-139571924 | p.A89A | 1 |
chr9:139571494-139571494 | p.G137G | 1 |
chr9:139571943-139571943 | p.P83fs*22 | 1 |
chr9:139568283-139568283 | p.R253M | 1 |
chr9:139571516-139571516 | p.G130D | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   | 1 |   | 4 | 1 |   | 1 |   | 1 |   |   | 2 |   |   |   | 1 | 4 | 3 |   | 3 |
# mutation |   | 1 |   | 4 | 1 |   | 1 |   | 1 |   |   | 2 |   |   |   | 1 | 4 | 3 |   | 3 |
nonsynonymous SNV |   |   |   | 2 | 1 |   | 1 |   |   |   |   | 2 |   |   |   | 1 | 2 |   |   | 2 |
synonymous SNV |   | 1 |   | 2 |   |   |   |   | 1 |   |   |   |   |   |   |   | 2 | 3 |   | 1 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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Top 10 SNVs Having the Most Samples in TCGA data |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr9:139568309 | p.L212L,AGPAT2 | 2 |
chr9:139571064 | p.G187G | 2 |
chr9:139571494 | p.S100N,AGPAT2 | 1 |
chr9:139571495 | p.P91S,AGPAT2 | 1 |
chr9:139571543 | p.A89A,AGPAT2 | 1 |
chr9:139568283 | p.R68R,AGPAT2 | 1 |
chr9:139571560 | p.R221M,AGPAT2 | 1 |
chr9:139571564 | p.G64C,AGPAT2 | 1 |
chr9:139569207 | p.L36Q,AGPAT2 | 1 |
chr9:139571892 | p.K182M,AGPAT2 | 1 |
Other DBs for Point Mutations |
Copy Number for AGPAT2 in TCGA |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for AGPAT2 |
Gene Expression in Cancer Cell-lines (CCLE) |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
Differential Gene Expression in Primary Tumors (TCGA) |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-Expressed gene's network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
AGPAT2,BCL7C,C7orf50,C9orf142,C9orf16,DNLZ,EDF1, EGFL7,FBXW5,FKBP2,GUK1,JOSD2,MRPL41,MRPL53, NDUFS7,NOXA1,PHPT1,PRDX5,SSNA1,ZDHHC12,ZNHIT1 | ACOT2,AGPAT2,ALDH2,ANXA6,AQP7,AVPI1,BOK, ADIRF,C14orf180,CAMK1,CEBPA,CIDEC,DTX1,FAH, GPX4,GYPC,HEPN1,LIPE,PLA2G16,PNPLA2,TMEM132C |
AGPAT2,ARRDC1,C9orf142,C9orf89,DOLPP1,EDF1,EXD3, FA2H,HDHD3,LOC100271831,NDOR1,POLD4,SH3GLB2,SIRT6, SIRT7,SLC22A18,SSNA1,TMEM54,TNNI3,TOR2A,TRIM15 | ABHD12,ACAA1,AGPAT2,MISP,C1orf106,CEBPG,CLRN3, DOLPP1,EZR,GDPD2,KALRN,MALL,MOGAT3,POR, PRR13,PTPRH,RAB8A,SLC9A3R1,SULT1A2,TMEM82,TOM1 |
Co-Expressed gene's Protein-protein interaction Network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for AGPAT2 |
There's no related Drug. |
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Cross referenced IDs for AGPAT2 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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