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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GPAT2 |
Basic gene info. | Gene symbol | GPAT2 |
Gene name | glycerol-3-phosphate acyltransferase 2, mitochondrial | |
Synonyms | CT123 | |
Cytomap | UCSC genome browser: 2q11.1 | |
Genomic location | chr2 :96687693-96700727 | |
Type of gene | protein-coding | |
RefGenes | NM_207328.2, | |
Ensembl id | ENSG00000186281 | |
Description | GPAT-2cancer/testis antigen 123xGPAT1 | |
Modification date | 20141207 | |
dbXrefs | HGNC : HGNC | |
Ensembl : ENSG00000186281 | ||
HPRD : 14089 | ||
Vega : OTTHUMG00000155208 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GPAT2 | |
BioGPS: 150763 | ||
Gene Expression Atlas: ENSG00000186281 | ||
The Human Protein Atlas: ENSG00000186281 | ||
Pathway | NCI Pathway Interaction Database: GPAT2 | |
KEGG: GPAT2 | ||
REACTOME: GPAT2 | ||
ConsensusPathDB | ||
Pathway Commons: GPAT2 | ||
Metabolism | MetaCyc: GPAT2 | |
HUMANCyc: GPAT2 | ||
Regulation | Ensembl's Regulation: ENSG00000186281 | |
miRBase: chr2 :96,687,693-96,700,727 | ||
TargetScan: NM_207328 | ||
cisRED: ENSG00000186281 | ||
Context | iHOP: GPAT2 | |
cancer metabolism search in PubMed: GPAT2 | ||
UCL Cancer Institute: GPAT2 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for GPAT2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GPAT2 |
Familial Cancer Database: GPAT2 |
* This gene is included in those cancer gene databases. |
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: GPAT2 |
MedGen: GPAT2 (Human Medical Genetics with Condition) | |
ClinVar: GPAT2 | |
Phenotype | MGI: GPAT2 (International Mouse Phenotyping Consortium) |
PhenomicDB: GPAT2 |
Mutations for GPAT2 |
* 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 GPAT2 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=38) | (# total SNVs=15) |
(# total SNVs=2) | (# 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 |
chr2:96688929-96688929 | p.R692C | 11 |
chr2:96697827-96697827 | p.R44H | 2 |
chr2:96696530-96696530 | p.C107fs*35 | 2 |
chr2:96689176-96689176 | p.R637W | 2 |
chr2:96697056-96697056 | p.T68T | 2 |
chr2:96687959-96687959 | p.L779Q | 2 |
chr2:96690401-96690401 | p.F481F | 2 |
chr2:96690528-96690528 | p.H474R | 2 |
chr2:96687999-96687999 | p.A766T | 1 |
chr2:96690533-96690533 | p.F472L | 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 | 4 | 2 | 1 | 4 | 1 |   | 4 |   | 2 |   |   | 4 | 2 |   |   |   | 6 | 3 | 1 | 10 |
# mutation | 4 | 2 | 1 | 4 | 1 |   | 5 |   | 1 |   |   | 5 | 2 |   |   |   | 6 | 3 | 1 | 12 |
nonsynonymous SNV | 4 |   | 1 | 4 | 1 |   | 2 |   |   |   |   | 4 | 2 |   |   |   | 6 | 2 | 1 | 5 |
synonymous SNV |   | 2 |   |   |   |   | 3 |   | 1 |   |   | 1 |   |   |   |   |   | 1 |   | 7 |
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 |
chr2:96691942 | p.F382L | 2 |
chr2:96697056 | p.T68T | 2 |
chr2:96688770 | p.D663D | 1 |
chr2:96691751 | p.V516V | 1 |
chr2:96689676 | p.P45L | 1 |
chr2:96690378 | p.T660T | 1 |
chr2:96688908 | p.S503N | 1 |
chr2:96689735 | p.R44H | 1 |
chr2:96690383 | p.W653C | 1 |
chr2:96688915 | p.L489Q | 1 |
Other DBs for Point Mutations |
Copy Number for GPAT2 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 GPAT2 |
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 |
BTN1A1,CD14,CD180,EDN3,GNLY,GPAT2,IGFL4, KIR3DX1,LIPG,MRGPRX3,NOS1,OLAH,PDE11A,PGA5, PTN,SST,TGFBR2,TMEM100,TMEM233,VNN1,XDH | AIFM3,ANKRD13D,MFSD12,CEMP1,CNPY3,CORO7,GBAP1, GPAT2,MTMR14,NAGK,NAGPA,OSCAR,PLD3,PNPLA6, PQLC2,PRAM1,INAFM1,SIPA1,TCIRG1,TNFRSF14,WASH5P |
ARSF,TOPAZ1,CST9,F7,FATE1,SPATA31D4,GPAT2, HLA-DQA2,HLA-DRB6,KRTAP10-8,LDHAL6A,LOC162632,MMP27,MMP8, OPCML,OR13C5,OR3A4P,OR51M1,PER4,SDK2,TYMP | ABHD12B,ASIC4,ALG12,ATP2A3,CLN3,GAS6,GPAT2, SLC52A2,HS3ST2,HSD11B2,ILDR1,KRT37,MMP9,MTNR1A, PRSS21,PYGL,RDH13,RIN1,SLC35A4,TMEM44,ZBTB42 |
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 GPAT2 |
There's no related Drug. |
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Cross referenced IDs for GPAT2 |
* 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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