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 PPARA
Basic gene info.Gene symbolPPARA
Gene nameperoxisome proliferator-activated receptor alpha
SynonymsNR1C1|PPAR|PPARalpha|hPPAR
CytomapUCSC genome browser: 22q13.31
Genomic locationchr22 :46546498-46639653
Type of geneprotein-coding
RefGenesNM_001001928.2,
NM_005036.4,NM_001001929.2,NM_001001930.2,NM_032644.3,
Ensembl idENSG00000186951
DescriptionPPAR-alphanuclear receptor subfamily 1 group C member 1peroxisome proliferative activated receptor, alphaperoxisome proliferator-activated nuclear receptor alpha variant 3
Modification date20141222
dbXrefs MIM : 170998
HGNC : HGNC
Ensembl : ENSG00000186951
HPRD : 01369
Vega : OTTHUMG00000150443
ProteinUniProt: Q07869
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PPARA
BioGPS: 5465
Gene Expression Atlas: ENSG00000186951
The Human Protein Atlas: ENSG00000186951
PathwayNCI Pathway Interaction Database: PPARA
KEGG: PPARA
REACTOME: PPARA
ConsensusPathDB
Pathway Commons: PPARA
MetabolismMetaCyc: PPARA
HUMANCyc: PPARA
RegulationEnsembl's Regulation: ENSG00000186951
miRBase: chr22 :46,546,498-46,639,653
TargetScan: NM_001001928
cisRED: ENSG00000186951
ContextiHOP: PPARA
cancer metabolism search in PubMed: PPARA
UCL Cancer Institute: PPARA
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PPARA in cancer cell metabolism1. Wang W-LW, Welsh J, Tenniswood M (2013) 1, 25-Dihydroxyvitamin D 3 modulates lipid metabolism in prostate cancer cells through miRNA mediated regulation of PPARA. The Journal of steroid biochemistry and molecular biology 136: 247-251. go to article

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Phenotypic Information for PPARA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PPARA
Familial Cancer Database: PPARA
* 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 170998; gene+phenotype.
Orphanet
DiseaseKEGG Disease: PPARA
MedGen: PPARA (Human Medical Genetics with Condition)
ClinVar: PPARA
PhenotypeMGI: PPARA (International Mouse Phenotyping Consortium)
PhenomicDB: PPARA

Mutations for PPARA
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryPPARAchr224657272046572740chr224625913546259155
ovaryPPARAchr224657982446579844CYTH4chr223769935337699373
ovaryPPARAchr224659832246598342chr224626048846260508
ovaryPPARAchr224663436746634387PPARAchr224663442846634448
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 PPARA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF911067PPARA496224655913346559225PPARA95392224655306446553360
AA807786PPARA8135224663768846637815PPARA133454224663736946637692
AI079573PPARA1164224663764846637811AP2M11625383183901431183901807

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      2   1  2   
GAIN (# sample)             2   
LOSS (# sample)      2   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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=4)
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
chr22:46614210-46614212p.R141delR2
chr22:46614211-46614211p.R141C2
chr22:46628123-46628123p.I382I2
chr22:46627961-46627961p.D328D2
chr22:46614234-46614234p.K148N2
chr22:46628131-46628131p.C385S2
chr22:46628050-46628050p.K358R2
chr22:46611088-46611088p.S76L2
chr22:46627814-46627814p.T279T2
chr22:46615714-46615714p.R172C2

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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
# sample 1 71   1  321  14415
# mutation 1 71   1  321  13416
nonsynonymous SNV 1 51      111  7311
synonymous SNV   2    1  21   61 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
chr22:46611088p.S76L,PPARA2
chr22:46627961p.D328D,PPARA2
chr22:46594453p.G42S,PPARA1
chr22:46628050p.L132L,PPARA1
chr22:46611192p.L344L,PPARA1
chr22:46615710p.G50G,PPARA1
chr22:46594462p.R141C,PPARA1
chr22:46628055p.K358E,PPARA1
chr22:46614165p.G58A,PPARA1
chr22:46615854p.S142I,PPARA1

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 PPARA 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 PPARA

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

ANKRD36BP1,ARHGAP21,CCDC82,CHST3,CLCN4,CREB3L2,FMNL2,
FNDC3B,IFNAR2,JOSD1,JRKL,KIAA1804,MAML2,MRAS,
NCK1,PKDREJ,PPARA,PTPN14,SOS1,TCF20,ZNF462
ACAT1,ADHFE1,ATP5B,TCAIM,ADCK3,ETFDH,HADHB,
HECTD1,KIAA0368,L2HGDH,NRD1,PDHX,PHYH,PPARA,
RMND5A,RRAGD,SLC2A4,SLC41A1,SOX6,SUCLA2,UQCRC2

ANKRD17,C9orf129,CGN,CMTM4,DENND4C,ENTPD5,INADL,
KIAA1109,KIAA1671,KIAA2018,MAGI3,MYO7B,PPARA,PTPRF,
PUM1,RBM47,RREB1,SH3D19,SPG11,TCF20,ZBED4
AGPAT3,ALDH18A1,ATP1A1,DNMBP,DOCK5,KBTBD11,KIF3B,
MARCH6,NHSL1,PLXNA2,POR,PPARA,PTPRK,SEMA6A,
TGOLN2,TNIK,UBE4A,VAV2,VIL1,ZCCHC14,ZZEF1
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 PPARA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q07869; -.
ChemistryChEMBL CHEMBL239; -.
ChemistryGuidetoPHARMACOLOGY 593; -.
Organism-specific databasesPharmGKB PA280; -.
Organism-specific databasesCTD 5465; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00636peroxisome proliferator-activated receptor alphaapprovedClofibrate
DB01039peroxisome proliferator-activated receptor alphaapprovedFenofibrate
DB01241peroxisome proliferator-activated receptor alphaapprovedGemfibrozil
DB01393peroxisome proliferator-activated receptor alphaapprovedBezafibrate
DB01890peroxisome proliferator-activated receptor alphaexperimentalDeoxy-Bigchap
DB07215peroxisome proliferator-activated receptor alphaexperimental2-METHYL-2-(4-{[({4-METHYL-2-[4-(TRIFLUOROMETHYL)PHENYL]-1,3-THIAZOL-5-YL}CARBONYL)AMINO]METHYL}PHENOXY)PROPANOIC ACID
DB07724peroxisome proliferator-activated receptor alphaexperimental3-{5-methoxy-1-[(4-methoxyphenyl)sulfonyl]-1H-indol-3-yl}propanoic acid
DB08483peroxisome proliferator-activated receptor alphaexperimental(2S)-2-methoxy-3-{4-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl)ethoxy]-1-benzothiophen-7-yl}propanoic acid
DB00724peroxisome proliferator-activated receptor alphaapproved; investigationalImiquimod


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Cross referenced IDs for PPARA
* 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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