Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 GPAM
Basic gene info.Gene symbolGPAM
Gene nameglycerol-3-phosphate acyltransferase, mitochondrial
SynonymsGPAT|GPAT1
CytomapUCSC genome browser: 10q25.2
Genomic locationchr10 :113909621-113943537
Type of geneprotein-coding
RefGenesNM_001244949.1,
NM_020918.5,
Ensembl idENSG00000119927
DescriptionGPAT-1glycerol 3-phosphate acyltransferase, mitochondrialglycerol-3-phosphate acyltransferase 1, mitochondrial
Modification date20141207
dbXrefs MIM : 602395
HGNC : HGNC
Ensembl : ENSG00000119927
HPRD : 03865
Vega : OTTHUMG00000019055
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPAM
BioGPS: 57678
Gene Expression Atlas: ENSG00000119927
The Human Protein Atlas: ENSG00000119927
PathwayNCI Pathway Interaction Database: GPAM
KEGG: GPAM
REACTOME: GPAM
ConsensusPathDB
Pathway Commons: GPAM
MetabolismMetaCyc: GPAM
HUMANCyc: GPAM
RegulationEnsembl's Regulation: ENSG00000119927
miRBase: chr10 :113,909,621-113,943,537
TargetScan: NM_001244949
cisRED: ENSG00000119927
ContextiHOP: GPAM
cancer metabolism search in PubMed: GPAM
UCL Cancer Institute: GPAM
Assigned class in ccmGDBC

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Phenotypic Information for GPAM(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPAM
Familial Cancer Database: GPAM
* 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: GPAM
MedGen: GPAM (Human Medical Genetics with Condition)
ClinVar: GPAM
PhenotypeMGI: GPAM (International Mouse Phenotyping Consortium)
PhenomicDB: GPAM

Mutations for GPAM
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryGPAMchr10113935444113935464GPAMchr10113935532113935552
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GPAM related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM710854GPAM132410113915622113917140PRKCB324419162423128124231376

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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=50)
Stat. for Synonymous SNVs
(# total SNVs=22)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=2)

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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
chr10:113921449-113921449p.C490C4
chr10:113913352-113913352p.R815*3
chr10:113924283-113924283p.R436K3
chr10:113932065-113932065p.P223P3
chr10:113920419-113920419p.E568K3
chr10:113921450-113921450p.C490F3
chr10:113918114-113918114p.V647G2
chr10:113928680-113928680p.F275F2
chr10:113941536-113941536p.E3K2
chr10:113928110-113928110p.Y356C2

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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
# sample12 7  2 2  742 146111
# mutation22 7  2 2  742 167113
nonsynonymous SNV 1 5  2 1  422 147 9
synonymous SNV21 2    1  32   2 14
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
chr10:113920419p.F275F,GPAM2
chr10:113921449p.C490C,GPAM2
chr10:113928680p.E568K,GPAM2
chr10:113924352p.T761T,GPAM1
chr10:113932005p.L540L,GPAM1
chr10:113915727p.V112I,GPAM1
chr10:113933596p.R108H,GPAM1
chr10:113920368p.P745H,GPAM1
chr10:113926232p.V533V,GPAM1
chr10:113932026p.A250S,GPAM1

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 GPAM 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 GPAM

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

ACVR1C,ADH1B,ADIPOQ,AOC3,AQP7,AQPEP,CIDEC,
GLYAT,GPAM,GPD1,HEPACAM,HEPN1,KCNIP2,KLB,
LEP,LIPE,PLIN1,PLIN4,SLC19A3,SORBS1,TMEM132C
ABCD2,ACER3,ACO1,ACSL1,ADIPOR2,ADRBK2,DMGDH,
ESYT1,GPAM,HRASLS5,LPL,SLC25A51,MMD,MARC1,
MRAS,PEX19,PLIN1,PRKAR2B,PYGL,TSPAN3,VKORC1L1

ADH1B,ADIPOQ,AQP7,CD300LG,CD36,FABP4,GLYAT,
GPAM,HEPACAM,KCNIP2,LEP,LGALS12,LIPE,LOC339524,
MRAP,PLIN1,PLIN4,SCN4A,THRSP,TTTY9B,TUSC5
ADIPOQ,CIDEA,DGAT2,FABP4,FCN2,G0S2,GPAM,
KCNIP2,KRT79,LGALS12,LOC283392,LPL,MRAP,NAT8L,
PFKFB1,PLIN1,SAA1,SCD,SLC7A10,THRSP,TUSC5
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 GPAM


There's no related Drug.
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Cross referenced IDs for GPAM
* 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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