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 PPARGC1A
Basic gene info.Gene symbolPPARGC1A
Gene nameperoxisome proliferator-activated receptor gamma, coactivator 1 alpha
SynonymsLEM6|PGC-1(alpha)|PGC-1v|PGC1|PGC1A|PPARGC1
CytomapUCSC genome browser: 4p15.1
Genomic locationchr4 :23793643-23891700
Type of geneprotein-coding
RefGenesNM_013261.3,
Ensembl idENSG00000109819
DescriptionL-PGC-1alphaPGC-1-alphaPPAR gamma coactivator variant formPPARGC-1-alphaligand effect modulator-6peroxisome proliferator-activated receptor gamma coactivator 1 alpha transcript variant B4peroxisome proliferator-activated receptor gamma coactivator 1
Modification date20141222
dbXrefs MIM : 604517
HGNC : HGNC
Ensembl : ENSG00000109819
HPRD : 05155
Vega : OTTHUMG00000097747
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PPARGC1A
BioGPS: 10891
Gene Expression Atlas: ENSG00000109819
The Human Protein Atlas: ENSG00000109819
PathwayNCI Pathway Interaction Database: PPARGC1A
KEGG: PPARGC1A
REACTOME: PPARGC1A
ConsensusPathDB
Pathway Commons: PPARGC1A
MetabolismMetaCyc: PPARGC1A
HUMANCyc: PPARGC1A
RegulationEnsembl's Regulation: ENSG00000109819
miRBase: chr4 :23,793,643-23,891,700
TargetScan: NM_013261
cisRED: ENSG00000109819
ContextiHOP: PPARGC1A
cancer metabolism search in PubMed: PPARGC1A
UCL Cancer Institute: PPARGC1A
Assigned class in ccmGDBC

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Phenotypic Information for PPARGC1A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PPARGC1A
Familial Cancer Database: PPARGC1A
* 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
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PPARGC1A
MedGen: PPARGC1A (Human Medical Genetics with Condition)
ClinVar: PPARGC1A
PhenotypeMGI: PPARGC1A (International Mouse Phenotyping Consortium)
PhenomicDB: PPARGC1A

Mutations for PPARGC1A
* 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 PPARGC1A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA047637PPARGC1A127042386571023865979NXN26744617702928703105

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample 1    1          
GAIN (# sample)      1          
LOSS (# sample) 1               
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=99)
Stat. for Synonymous SNVs
(# total SNVs=29)
Stat. for Deletions
(# total SNVs=1)
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
chr4:23803371-23803371p.S759P5
chr4:23797452-23797452p.R797H2
chr4:23831086-23831086p.K184N2
chr4:23825936-23825936p.R282C2
chr4:23830042-23830042p.S246S2
chr4:23830129-23830129p.N217N2
chr4:23816064-23816064p.G348R2
chr4:23815648-23815648p.D486E2
chr4:23886512-23886512p.L33I2
chr4:23803936-23803936p.I684I2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample14 19  3 41 1764 11717 11
# mutation24 17  3 41 1964 12017 16
nonsynonymous SNV24 14  3 31 1253  1411 11
synonymous SNV   3    1  711 166 5
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
chr4:23803371p.S759P4
chr4:23886493p.S246S2
chr4:23830129p.Y355N2
chr4:23816043p.N217N2
chr4:23830042p.R711W2
chr4:23803857p.S39C2
chr4:23814698p.H169H1
chr4:23815983p.R694M1
chr4:23831131p.D32E1
chr4:23797452p.N615T1

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 PPARGC1A 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 PPARGC1A

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

C2orf40,CA13,CHRM3,FBN3,GJD2,KCNK5,KLF5,
LOC154822,MCTP2,MFSD4,PDE4D,PLA2G4A,PPARGC1A,SCEL,
SLAIN1,SLC7A5,SMOC1,SOX6,TMEM213,TRIM2,WNT1
ADSSL1,AGL,AKAP6,ASB14,ASB8,METTL21C,CA3,
COQ10A,FXR1,KBTBD12,KIF1B,KLHL33,MYOM1,PAIP2B,
PPARGC1A,SPTB,TMEM182,TMEM52,TRIM55,USP13,XPO4

ACADSB,ACO2,ATP5B,ATP8A1,B4GALNT2,C12orf49,CPEB3,
CS,GAK,GLYATL2,GOT1,GPR125,HEXB,OR13C4,
PPARGC1A,RAB5B,RBM47,SEL1L3,SLC5A8,SLC6A18,TBC1D14
ABCA5,ACVR1B,ACVR1C,EFCAB5,EFTUD1,EPB41L4B,FHDC1,
MLLT4,NPAS2,NR5A2,PPARGC1A,PPFIBP2,RAB11FIP1,RAVER2,
SGK223,SLC22A23,SNX30,TOX3,VDR,VSIG10,ZNF91
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 PPARGC1A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01132peroxisome proliferator-activated receptor gamma, coactivator 1 alphaapproved; investigationalPioglitazone


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Cross referenced IDs for PPARGC1A
* 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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