Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for GPAT2
Basic gene info.Gene symbolGPAT2
Gene nameglycerol-3-phosphate acyltransferase 2, mitochondrial
SynonymsCT123
CytomapUCSC genome browser: 2q11.1
Genomic locationchr2 :96687693-96700727
Type of geneprotein-coding
RefGenesNM_207328.2,
Ensembl idENSG00000186281
DescriptionGPAT-2cancer/testis antigen 123xGPAT1
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000186281
HPRD : 14089
Vega : OTTHUMG00000155208
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPAT2
BioGPS: 150763
Gene Expression Atlas: ENSG00000186281
The Human Protein Atlas: ENSG00000186281
PathwayNCI Pathway Interaction Database: GPAT2
KEGG: GPAT2
REACTOME: GPAT2
ConsensusPathDB
Pathway Commons: GPAT2
MetabolismMetaCyc: GPAT2
HUMANCyc: GPAT2
RegulationEnsembl's Regulation: ENSG00000186281
miRBase: chr2 :96,687,693-96,700,727
TargetScan: NM_207328
cisRED: ENSG00000186281
ContextiHOP: GPAT2
cancer metabolism search in PubMed: GPAT2
UCL Cancer Institute: GPAT2
Assigned class in ccmGDBC

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Phenotypic Information for GPAT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPAT2
Familial Cancer Database: GPAT2
* This gene is included in those cancer gene databases.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
KEGG_GLYCEROLIPID_METABOLISM
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GPAT2
MedGen: GPAT2 (Human Medical Genetics with Condition)
ClinVar: GPAT2
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GPAT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=11

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=38)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr2:96688929-96688929p.R692C11
chr2:96690528-96690528p.H474R2
chr2:96697827-96697827p.R44H2
chr2:96696530-96696530p.C107fs*352
chr2:96689176-96689176p.R637W2
chr2:96697056-96697056p.T68T2
chr2:96687959-96687959p.L779Q2
chr2:96690401-96690401p.F481F2
chr2:96689105-96689105p.T660T1
chr2:96691752-96691752p.I388I1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample42141 4 2  42   63110
# mutation42141 5 1  52   63112
nonsynonymous SNV4 141 2    42   6215
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr2:96691942p.F382L2
chr2:96697056p.T68T2
chr2:96687911p.R790R1
chr2:96690546p.E631Q1
chr2:96689105p.T463K1
chr2:96697827p.Q782E1
chr2:96690055p.S611F1
chr2:96687925p.G456E1
chr2:96690561p.R769R1
chr2:96689126p.Q609K1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

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
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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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

: Open all cross reference information



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