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 PPARG
Basic gene info.Gene symbolPPARG
Gene nameperoxisome proliferator-activated receptor gamma
SynonymsCIMT1|GLM1|NR1C3|PPARG1|PPARG2|PPARgamma
CytomapUCSC genome browser: 3p25
Genomic locationchr3 :12329348-12475855
Type of geneprotein-coding
RefGenesNM_005037.5,
NM_015869.4,NM_138711.3,NM_138712.3,
Ensembl idENSG00000132170
DescriptionPPAR-gammanuclear receptor subfamily 1 group C member 3peroxisome proliferator-activated nuclear receptor gamma variant 1
Modification date20141222
dbXrefs MIM : 601487
HGNC : HGNC
Ensembl : ENSG00000132170
HPRD : 03288
Vega : OTTHUMG00000129764
ProteinUniProt: P37231
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PPARG
BioGPS: 5468
Gene Expression Atlas: ENSG00000132170
The Human Protein Atlas: ENSG00000132170
PathwayNCI Pathway Interaction Database: PPARG
KEGG: PPARG
REACTOME: PPARG
ConsensusPathDB
Pathway Commons: PPARG
MetabolismMetaCyc: PPARG
HUMANCyc: PPARG
RegulationEnsembl's Regulation: ENSG00000132170
miRBase: chr3 :12,329,348-12,475,855
TargetScan: NM_005037
cisRED: ENSG00000132170
ContextiHOP: PPARG
cancer metabolism search in PubMed: PPARG
UCL Cancer Institute: PPARG
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PPARG in cancer cell metabolism1. Costa V, Gallo MA, Letizia F, Aprile M, Casamassimi A, et al. (2010) PPARG: gene expression regulation and next-generation sequencing for unsolved issues. PPAR research 2010. go to article
2. Sabatino L, Fucci A, Pancione M, Colantuoni V (2012) PPARG epigenetic deregulation and Its role in colorectal tumorigenesis. PPAR research 2012. go to article

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Phenotypic Information for PPARG(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PPARG
Familial Cancer Database: PPARG
* 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 137800; phenotype.
137800; phenotype.
601487; gene.
601487; gene.
601665; phenotype.
601665; phenotype.
604367; phenotype.
604367; phenotype.
606641; phenotype.
606641; phenotype.
609338; phenotype.
609338; phenotype.
Orphanet 251576; Gliosarcoma.
251576; Gliosarcoma.
251579; Giant cell glioblastoma.
251579; Giant cell glioblastoma.
79083; Familial partial lipodystrophy associated with PPARG mutations.
79083; Familial partial lipodystrophy associated with PPARG mutations.
DiseaseKEGG Disease: PPARG
MedGen: PPARG (Human Medical Genetics with Condition)
ClinVar: PPARG
PhenotypeMGI: PPARG (International Mouse Phenotyping Consortium)
PhenomicDB: PPARG

Mutations for PPARG
* 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
NSPPARGchr31236744412367444FAM208Achr35667958256679582
ovaryPPARGchr31241408312414103chr37393997573939995
ovaryPPARGchr31243139412431414PPARGchr31243165012431670
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 PPARG related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AY222643CREB3L213197137612896137686451PPARG319175531242120212475644
AY149631THADA1418524365523643823177PPARG4181444031236107112361330

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 # sample3       1       3
GAIN (# sample)3               3
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=34)
Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr3:12393098-12393098p.E3K3
chr3:12458488-12458488p.I369L2
chr3:12475557-12475557p.H477H2
chr3:12458305-12458305p.R308C2
chr3:12458497-12458497p.G372S2
chr3:12447447-12447447p.I229T2
chr3:12458323-12458323p.Q314E2
chr3:12447485-12447485p.L242V2
chr3:12447429-12447429p.A223V2
chr3:12447430-12447430p.A223A2

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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
# sample22 61   2  9 1 1142 8
# mutation22 61   2  9 1 1132 9
nonsynonymous SNV22 31   1  5   181 7
synonymous SNV   3    1  4 1  51 2
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
chr3:12458497p.G344S,PPARG2
chr3:12422837p.R57K,PPARG1
chr3:12475421p.L214V,PPARG1
chr3:12447430p.E369G,PPARG1
chr3:12393166p.P60A,PPARG1
chr3:12458442p.A235A,PPARG1
chr3:12422846p.S382S,PPARG1
chr3:12475528p.E73E,PPARG1
chr3:12447443p.I249N,PPARG1
chr3:12421229p.I388I,PPARG1

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 PPARG 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 PPARG

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,CCDC82,CFLAR,DAPK1,AMER1,FMNL2,GNPTAB,
KIAA0754,LIMS1,LOC400927,MAML2,MLXIP,MYO9B,NOTCH1,
PPARA,PPARGC1B,SFT2D2,MIEF1,TCF20,WWTR1,ZNF462
CAMSAP1,CLASP1,DMD,AGO2,FBXO10,HECTD1,HERC1,
KIAA0368,VWA8,KIAA1161,L2HGDH,LOC729082,MLXIP,NFIC,
NFIX,PCNT,PPARA,PPARGC1B,PRKAR2A,SATB1,UBR3

ATXN7,NOP9,C9orf129,DDX46,DOT1L,ETV3,FAM160A1,
GNA11,IPMK,MAP3K13,MDN1,MFSD9,MLXIP,NSD1,
PCNT,PDP2,PPARGC1B,RBM15,RNF168,RREB1,SERINC5
ARHGAP33,HECTD4,PROSER3,CAD,CEP152,DIP2A,GSE1,
KMT2B___KMT2D,NBPF10,NEURL4,PLXNB1,POLR3A,PPARGC1B,RBM33,
SUGP2,TRIO,CFAP44,WDR90,WHSC1,ZMIZ2,ZNF142
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 PPARG
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P37231; -.
ChemistryChEMBL CHEMBL2095162; -.
ChemistryGuidetoPHARMACOLOGY 595; -.
ChemistryBindingDB P37231; -.
ChemistryChEMBL CHEMBL2095162; -.
ChemistryGuidetoPHARMACOLOGY 595; -.
Organism-specific databasesPharmGKB PA281; -.
Organism-specific databasesPharmGKB PA281; -.
Organism-specific databasesCTD 5468; -.
Organism-specific databasesCTD 5468; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00159peroxisome proliferator-activated receptor gammaapproved; nutraceuticalIcosapent
DB00197peroxisome proliferator-activated receptor gammawithdrawnTroglitazone
DB00244peroxisome proliferator-activated receptor gammaapprovedMesalazine
DB00328peroxisome proliferator-activated receptor gammaapproved; investigationalIndomethacin
DB00412peroxisome proliferator-activated receptor gammaapproved; investigationalRosiglitazone
DB00731peroxisome proliferator-activated receptor gammaapproved; investigationalNateglinide
DB00795peroxisome proliferator-activated receptor gammaapprovedSulfasalazine
DB00912peroxisome proliferator-activated receptor gammaapproved; investigationalRepaglinide
DB00966peroxisome proliferator-activated receptor gammaapproved; investigationalTelmisartan
DB01014peroxisome proliferator-activated receptor gammaapproved; investigationalBalsalazide
DB01067peroxisome proliferator-activated receptor gammaapprovedGlipizide
DB01132peroxisome proliferator-activated receptor gammaapproved; investigationalPioglitazone
DB01252peroxisome proliferator-activated receptor gammaapproved; investigationalMitiglinide
DB01393peroxisome proliferator-activated receptor gammaapprovedBezafibrate
DB04270peroxisome proliferator-activated receptor gammaexperimental(S)-3-(4-(2-Carbazol-9-Yl-Ethoxy)-Phenyl)-2-Ethoxy-Propionic Acid
DB04689peroxisome proliferator-activated receptor gammaexperimental2-{5-[3-(6-BENZOYL-1-PROPYLNAPHTHALEN-2-YLOXY)PROPOXY]INDOL-1-YL}ETHANOIC ACID
DB06908peroxisome proliferator-activated receptor gammaexperimental(2S)-3-(1-{[2-(2-CHLOROPHENYL)-5-METHYL-1,3-OXAZOL-4-YL]METHYL}-1H-INDOL-5-YL)-2-ETHOXYPROPANOIC ACID
DB06926peroxisome proliferator-activated receptor gammaexperimental(9Z,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid
DB07053peroxisome proliferator-activated receptor gammaexperimental2-{5-[3-(7-PROPYL-3-TRIFLUOROMETHYLBENZO[D]ISOXAZOL-6-YLOXY)PROPOXY]INDOL-1-YL}ETHANOIC ACID
DB07111peroxisome proliferator-activated receptor gammaexperimental(4S,5E,7Z,10Z,13Z,16Z,19Z)-4-hydroxydocosa-5,7,10,13,16,19-hexaenoic acid
DB07172peroxisome proliferator-activated receptor gammaexperimental(5R,6E,8Z,11Z,14Z,17Z)-5-hydroxyicosa-6,8,11,14,17-pentaenoic acid
DB07208peroxisome proliferator-activated receptor gammaexperimental(8E,10S,12Z)-10-hydroxy-6-oxooctadeca-8,12-dienoic acid
DB07209peroxisome proliferator-activated receptor gammaexperimental(8R,9Z,12Z)-8-hydroxy-6-oxooctadeca-9,12-dienoic acid
DB07302peroxisome proliferator-activated receptor gammaexperimental(9S,10E,12Z)-9-hydroxyoctadeca-10,12-dienoic acid
DB07509peroxisome proliferator-activated receptor gammaexperimentaldifluoro(5-{2-[(5-octyl-1H-pyrrol-2-yl-kappaN)methylidene]-2H-pyrrol-5-yl-kappaN}pentanoato)boron
DB07675peroxisome proliferator-activated receptor gammaexperimental(2S)-2-ETHOXY-3-{4-[2-(10H-PHENOXAZIN-10-YL)ETHOXY]PHENYL}PROPANOIC ACID
DB07723peroxisome proliferator-activated receptor gammaexperimental3-(5-methoxy-1H-indol-3-yl)propanoic acid
DB07724peroxisome proliferator-activated receptor gammaexperimental3-{5-methoxy-1-[(4-methoxyphenyl)sulfonyl]-1H-indol-3-yl}propanoic acid
DB07842peroxisome proliferator-activated receptor gammaexperimental(2S)-2-(4-ethylphenoxy)-3-phenylpropanoic acid
DB07863peroxisome proliferator-activated receptor gammaexperimental2-chloro-5-nitro-N-phenylbenzamide
DB08121peroxisome proliferator-activated receptor gammaexperimental(2S)-2-(biphenyl-4-yloxy)-3-phenylpropanoic acid
DB08302peroxisome proliferator-activated receptor gammaexperimental3-[5-(2-nitropent-1-en-1-yl)furan-2-yl]benzoic acid
DB08402peroxisome proliferator-activated receptor gammaexperimental2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID
DB08435peroxisome proliferator-activated receptor gammaexperimental(5E,14E)-11-oxoprosta-5,9,12,14-tetraen-1-oic acid
DB08483peroxisome proliferator-activated receptor gammaexperimental(2S)-2-methoxy-3-{4-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl)ethoxy]-1-benzothiophen-7-yl}propanoic acid
DB08560peroxisome proliferator-activated receptor gammaexperimental3-FLUORO-N-[1-(4-FLUOROPHENYL)-3-(2-THIENYL)-1H-PYRAZOL-5-YL]BENZENESULFONAMIDE
DB08760peroxisome proliferator-activated receptor gammaexperimental(2S)-2-(4-chlorophenoxy)-3-phenylpropanoic acid
DB00755peroxisome proliferator-activated receptor gammaapproved; nutraceutical; investigationalTretinoin
DB00945peroxisome proliferator-activated receptor gammaapprovedAcetylsalicylic acid
DB00741peroxisome proliferator-activated receptor gammaapprovedHydrocortisone
DB00482peroxisome proliferator-activated receptor gammaapproved; investigationalCelecoxib


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Cross referenced IDs for PPARG
* 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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