Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 PPARG

Basic gene info.	Gene symbol	PPARG
	Gene name	peroxisome proliferator-activated receptor gamma
	Synonyms	CIMT1\|GLM1\|NR1C3\|PPARG1\|PPARG2\|PPARgamma
	Cytomap	UCSC genome browser: 3p25
	Genomic location	chr3 :12329348-12475855
	Type of gene	protein-coding
	RefGenes	NM_005037.5, NM_015869.4,NM_138711.3,NM_138712.3,
	Ensembl id	ENSG00000132170
	Description	PPAR-gammanuclear receptor subfamily 1 group C member 3peroxisome proliferator-activated nuclear receptor gamma variant 1
	Modification date	20141222
dbXrefs	MIM : 601487
	HGNC : HGNC
	Ensembl : ENSG00000132170
	HPRD : 03288
	Vega : OTTHUMG00000129764
Protein	UniProt: P37231 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PPARG
	BioGPS: 5468
	Gene Expression Atlas: ENSG00000132170
	The Human Protein Atlas: ENSG00000132170
Pathway	NCI Pathway Interaction Database: PPARG
	KEGG: PPARG
	REACTOME: PPARG
	ConsensusPathDB
	Pathway Commons: PPARG
Metabolism	MetaCyc: PPARG
	HUMANCyc: PPARG
Regulation	Ensembl's Regulation: ENSG00000132170
	miRBase: chr3 :12,329,348-12,475,855
	TargetScan: NM_005037
	cisRED: ENSG00000132170
Context	iHOP: PPARG
	cancer metabolism search in PubMed: PPARG
	UCL Cancer Institute: PPARG
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PPARG in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
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.
Disease	KEGG Disease: PPARG
	MedGen: PPARG (Human Medical Genetics with Condition)
	ClinVar: PPARG
Phenotype	MGI: PPARG (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
NS	PPARG	chr3	12367444	12367444	FAM208A	chr3	56679582	56679582
ovary	PPARG	chr3	12414083	12414103		chr3	73939975	73939995
ovary	PPARG	chr3	12431394	12431414	PPARG	chr3	12431650	12431670

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PPARG related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AY222643	CREB3L2	1	319	7	137612896	137686451	PPARG	319	1755	3	12421202	12475644
AY149631	THADA	1	4185	2	43655236	43823177	PPARG	4181	4440	3	12361071	12361330

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr3:12393098-12393098	p.E3K	3
chr3:12447429-12447429	p.A223V	2
chr3:12447430-12447430	p.A223A	2
chr3:12458488-12458488	p.I369L	2
chr3:12475557-12475557	p.H477H	2
chr3:12458305-12458305	p.R308C	2
chr3:12458497-12458497	p.G372S	2
chr3:12447447-12447447	p.I229T	2
chr3:12458323-12458323	p.Q314E	2
chr3:12447485-12447485	p.L242V	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2	2		6	1				2			9		1		1	14	2		8
# mutation	2	2		6	1				2			9		1		1	13	2		9
nonsynonymous SNV	2	2		3	1				1			5				1	8	1		7
synonymous SNV				3					1			4		1			5	1		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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr3:12458497	p.G344S,PPARG	2
chr3:12458253	p.R57K,PPARG	1
chr3:12421306	p.L214V,PPARG	1
chr3:12434237	p.E369G,PPARG	1
chr3:12458265	p.P60A,PPARG	1
chr3:12421355	p.A235A,PPARG	1
chr3:12458537	p.S382S,PPARG	1
chr3:12447398	p.I388I,PPARG	1
chr3:12458286	p.E73E,PPARG	1
chr3:12421374	p.I249N,PPARG	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P37231; -.
Chemistry	ChEMBL	CHEMBL2095162; -.
Chemistry	GuidetoPHARMACOLOGY	595; -.
Chemistry	BindingDB	P37231; -.
Chemistry	ChEMBL	CHEMBL2095162; -.
Chemistry	GuidetoPHARMACOLOGY	595; -.
Organism-specific databases	PharmGKB	PA281; -.
Organism-specific databases	PharmGKB	PA281; -.
Organism-specific databases	CTD	5468; -.
Organism-specific databases	CTD	5468; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00159	peroxisome proliferator-activated receptor gamma	approved; nutraceutical	Icosapent
DB00197	peroxisome proliferator-activated receptor gamma	withdrawn	Troglitazone
DB00244	peroxisome proliferator-activated receptor gamma	approved	Mesalazine
DB00328	peroxisome proliferator-activated receptor gamma	approved; investigational	Indomethacin
DB00412	peroxisome proliferator-activated receptor gamma	approved; investigational	Rosiglitazone
DB00731	peroxisome proliferator-activated receptor gamma	approved; investigational	Nateglinide
DB00795	peroxisome proliferator-activated receptor gamma	approved	Sulfasalazine
DB00912	peroxisome proliferator-activated receptor gamma	approved; investigational	Repaglinide
DB00966	peroxisome proliferator-activated receptor gamma	approved; investigational	Telmisartan
DB01014	peroxisome proliferator-activated receptor gamma	approved; investigational	Balsalazide
DB01067	peroxisome proliferator-activated receptor gamma	approved	Glipizide
DB01132	peroxisome proliferator-activated receptor gamma	approved; investigational	Pioglitazone
DB01252	peroxisome proliferator-activated receptor gamma	approved; investigational	Mitiglinide
DB01393	peroxisome proliferator-activated receptor gamma	approved	Bezafibrate
DB04270	peroxisome proliferator-activated receptor gamma	experimental	(S)-3-(4-(2-Carbazol-9-Yl-Ethoxy)-Phenyl)-2-Ethoxy-Propionic Acid
DB04689	peroxisome proliferator-activated receptor gamma	experimental	2-{5-[3-(6-BENZOYL-1-PROPYLNAPHTHALEN-2-YLOXY)PROPOXY]INDOL-1-YL}ETHANOIC ACID
DB06908	peroxisome proliferator-activated receptor gamma	experimental	(2S)-3-(1-{[2-(2-CHLOROPHENYL)-5-METHYL-1,3-OXAZOL-4-YL]METHYL}-1H-INDOL-5-YL)-2-ETHOXYPROPANOIC ACID
DB06926	peroxisome proliferator-activated receptor gamma	experimental	(9Z,11E,13S)-13-hydroxyoctadeca-9,11-dienoic acid
DB07053	peroxisome proliferator-activated receptor gamma	experimental	2-{5-[3-(7-PROPYL-3-TRIFLUOROMETHYLBENZO[D]ISOXAZOL-6-YLOXY)PROPOXY]INDOL-1-YL}ETHANOIC ACID
DB07111	peroxisome proliferator-activated receptor gamma	experimental	(4S,5E,7Z,10Z,13Z,16Z,19Z)-4-hydroxydocosa-5,7,10,13,16,19-hexaenoic acid
DB07172	peroxisome proliferator-activated receptor gamma	experimental	(5R,6E,8Z,11Z,14Z,17Z)-5-hydroxyicosa-6,8,11,14,17-pentaenoic acid
DB07208	peroxisome proliferator-activated receptor gamma	experimental	(8E,10S,12Z)-10-hydroxy-6-oxooctadeca-8,12-dienoic acid
DB07209	peroxisome proliferator-activated receptor gamma	experimental	(8R,9Z,12Z)-8-hydroxy-6-oxooctadeca-9,12-dienoic acid
DB07302	peroxisome proliferator-activated receptor gamma	experimental	(9S,10E,12Z)-9-hydroxyoctadeca-10,12-dienoic acid
DB07509	peroxisome proliferator-activated receptor gamma	experimental	difluoro(5-{2-[(5-octyl-1H-pyrrol-2-yl-kappaN)methylidene]-2H-pyrrol-5-yl-kappaN}pentanoato)boron
DB07675	peroxisome proliferator-activated receptor gamma	experimental	(2S)-2-ETHOXY-3-{4-[2-(10H-PHENOXAZIN-10-YL)ETHOXY]PHENYL}PROPANOIC ACID
DB07723	peroxisome proliferator-activated receptor gamma	experimental	3-(5-methoxy-1H-indol-3-yl)propanoic acid
DB07724	peroxisome proliferator-activated receptor gamma	experimental	3-{5-methoxy-1-[(4-methoxyphenyl)sulfonyl]-1H-indol-3-yl}propanoic acid
DB07842	peroxisome proliferator-activated receptor gamma	experimental	(2S)-2-(4-ethylphenoxy)-3-phenylpropanoic acid
DB07863	peroxisome proliferator-activated receptor gamma	experimental	2-chloro-5-nitro-N-phenylbenzamide
DB08121	peroxisome proliferator-activated receptor gamma	experimental	(2S)-2-(biphenyl-4-yloxy)-3-phenylpropanoic acid
DB08302	peroxisome proliferator-activated receptor gamma	experimental	3-[5-(2-nitropent-1-en-1-yl)furan-2-yl]benzoic acid
DB08402	peroxisome proliferator-activated receptor gamma	experimental	2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID
DB08435	peroxisome proliferator-activated receptor gamma	experimental	(5E,14E)-11-oxoprosta-5,9,12,14-tetraen-1-oic acid
DB08483	peroxisome proliferator-activated receptor gamma	experimental	(2S)-2-methoxy-3-{4-[2-(5-methyl-2-phenyl-1,3-oxazol-4-yl)ethoxy]-1-benzothiophen-7-yl}propanoic acid
DB08560	peroxisome proliferator-activated receptor gamma	experimental	3-FLUORO-N-[1-(4-FLUOROPHENYL)-3-(2-THIENYL)-1H-PYRAZOL-5-YL]BENZENESULFONAMIDE
DB08760	peroxisome proliferator-activated receptor gamma	experimental	(2S)-2-(4-chlorophenoxy)-3-phenylpropanoic acid
DB00755	peroxisome proliferator-activated receptor gamma	approved; nutraceutical; investigational	Tretinoin
DB00945	peroxisome proliferator-activated receptor gamma	approved	Acetylsalicylic acid
DB00741	peroxisome proliferator-activated receptor gamma	approved	Hydrocortisone
DB00482	peroxisome proliferator-activated receptor gamma	approved; investigational	Celecoxib

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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