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 GSTP1

Basic gene info.	Gene symbol	GSTP1
	Gene name	glutathione S-transferase pi 1
	Synonyms	DFN7\|FAEES3\|GST3\|GSTP\|HEL-S-22\|PI
	Cytomap	UCSC genome browser: 11q13
	Genomic location	chr11 :67351065-67354124
	Type of gene	protein-coding
	RefGenes	NM_000852.3,
	Ensembl id	ENSG00000084207
	Description	GST class-piGSTP1-1deafness, X-linked 7epididymis secretory protein Li 22fatty acid ethyl ester synthase IIIglutathione S-transferase P
	Modification date	20141222
dbXrefs	MIM : 134660
	HGNC : HGNC
	Ensembl : ENSG00000084207
	HPRD : 00614
	Vega : OTTHUMG00000137430
Protein	UniProt: P09211 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GSTP1
	BioGPS: 2950
	Gene Expression Atlas: ENSG00000084207
	The Human Protein Atlas: ENSG00000084207
Pathway	NCI Pathway Interaction Database: GSTP1
	KEGG: GSTP1
	REACTOME: GSTP1
	ConsensusPathDB
	Pathway Commons: GSTP1
Metabolism	MetaCyc: GSTP1
	HUMANCyc: GSTP1
Regulation	Ensembl's Regulation: ENSG00000084207
	miRBase: chr11 :67,351,065-67,354,124
	TargetScan: NM_000852
	cisRED: ENSG00000084207
Context	iHOP: GSTP1
	cancer metabolism search in PubMed: GSTP1
	UCL Cancer Institute: GSTP1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GSTP1 in cancer cell metabolism	1. Yuan ZJ, Zhou WW, Liu W, Wu BP, Zhao J, et al. (2015) Association of GSTP1 and RRM1 Polymorphisms with the Response and Toxicity of Gemcitabine-cisplatin Combination Chemotherapy in Chinese Patients with Non-small Cell Lung Cancer. Asian Pac J Cancer Prev 16: 4347-4351. go to article 2. Hevir-Kene N, Rizner TL (2015) The endometrial cancer cell lines Ishikawa and HEC-1A, and the control cell line HIEEC, differ in expression of estrogen biosynthetic and metabolic genes, and in androstenedione and estrone-sulfate metabolism. Chem Biol Interact 234: 309-319. doi: 10.1016/j.cbi.2014.11.015. go to article

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Phenotypic Information for GSTP1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GSTP1
	Familial Cancer Database: GSTP1

* 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
KEGG_GLUTATHIONE_METABOLISM KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 KEGG_DRUG_METABOLISM_CYTOCHROME_P450

Others
OMIM	134660; gene.
Orphanet
Disease	KEGG Disease: GSTP1
	MedGen: GSTP1 (Human Medical Genetics with Condition)
	ClinVar: GSTP1
Phenotype	MGI: GSTP1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GSTP1

Mutations for GSTP1

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GSTP1 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
BG978110	GSTP1	27	204	11	67352170	67352713	PSMB1	205	459	6	170855254	170862345
AW263990	GSTP1	1	365	11	67353584	67354125	FAM53B	359	519	10	126310197	126310357
BF819091	GSTP1	28	355	11	67351613	67352713	XRCC5	351	547	2	217002818	217006020
AA535995	GSTP1	3	203	11	67353925	67354124	CTSA	192	251	20	44522645	44522704
BU527119	GSTP1	105	477	11	67353575	67354124	SLC26A4	468	494	7	107322541	107322567
AW206069	GSTP1	17	246	11	67353723	67354124	LAMA5	244	323	20	60900569	60900648
AW390894	GSTP1	19	175	11	67352682	67353878	WHSC1	164	304	4	1962760	1976611
AW390893	GSTP1	1	98	11	67352682	67353645	WHSC1	87	206	4	1962760	1962879

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

There's no copy number variation information in COSMIC data for this gene.

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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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=15)	Stat. for Synonymous SNVs (# total SNVs=13)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr11:67353985-67353985	p.L190L	2
chr11:67353970-67353970	p.S185S	2
chr11:67352191-67352191	p.D60E	2
chr11:67352198-67352198	p.L63M	1
chr11:67353675-67353675	p.G146V	1
chr11:67352199-67352199	p.L63P	1
chr11:67353865-67353865	p.S150S	1
chr11:67353993-67353993	p.F193S	1
chr11:67352214-67352214	p.T68S	1
chr11:67353898-67353898	p.L161L	1

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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	1							1		1	1	1			3	2		9
# mutation	3	2	1							1		1	1	1			4	2		9
nonsynonymous SNV	1	1								1		1	1				2	1		2
synonymous SNV	2	1	1											1			2	1		7

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
chr11:67353985	p.L190L	2
chr11:67352613	p.L134L	1
chr11:67353933	p.N201D	1
chr11:67352640	p.Q136Q	1
chr11:67353934	p.G140G	1
chr11:67353590	p.G146V	1
chr11:67353948	p.S150S	1
chr11:67353638	p.L161L	1
chr11:67353976	p.H163Y	1
chr11:67353646	p.G169G	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 GSTP1 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 GSTP1

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


BID,CEBPB,YBX3,FAM58A,GSTP1,HMGA1,LAD1, MAGOH,MRPS5,NMB,NPM3,POLR2F,PPP1R14B,RPS7, SHFM1,SNRPA,TMEM39B,UBE2E3,UQCRH,UQCRHL,YBX1	APOA1BP,ARF5,CFL1,CHCHD5,CNFN,FAM58A,FIBP, GSTP1,MOSPD3,MRPL52,MRPS21,NSMCE1,PPP4C,PSMG3, RHOC,SDF2,SF3B5,TMEM115,TMEM208,TRMT112,YIPF3

BANF1,TMEM258,ANAPC15,UQCC3,TMEM256,CDK2AP2,FAM96B, FAU,GLB1L2,GSTP1,MGST2,MRPL28,NT5C,NUDT8, POP7,PPP1CA,PPP1R14B,THOC6,PAM16,TMEM134,WIBG	APRT,TMEM258,C17orf49,C9orf16,CLPP,EIF3I,GADD45GIP1, GSTP1,IMP4,KRTCAP2,MRPL52,NAA10,NDUFA7,NDUFS6, NME2,POLR2L,POP7,SF3B5,SNRPB,TMEM11,TMEM147

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 GSTP1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P09211; -.
Chemistry	ChEMBL	CHEMBL3902; -.
Organism-specific databases	PharmGKB	PA29028; -.
Organism-specific databases	CTD	2950; -.

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
DB00143	glutathione S-transferase pi 1	approved; nutraceutical	Glutathione
DB01242	glutathione S-transferase pi 1	approved	Clomipramine
DB01834	glutathione S-transferase pi 1	experimental	(9r,10r)-9-(S-Glutathionyl)-10-Hydroxy-9,10-Dihydrophenanthrene
DB01915	glutathione S-transferase pi 1	experimental	S-Hydroxycysteine
DB02633	glutathione S-transferase pi 1	experimental	Cibacron Blue
DB03003	glutathione S-transferase pi 1	experimental	Glutathione Sulfonic Acid
DB03686	glutathione S-transferase pi 1	experimental	S-(P-Nitrobenzyl)Glutathione
DB03814	glutathione S-transferase pi 1	experimental	2-(N-Morpholino)-Ethanesulfonic Acid
DB04077	glutathione S-transferase pi 1	experimental	Glycerol
DB04132	glutathione S-transferase pi 1	experimental	S-Hexylglutathione
DB04339	glutathione S-transferase pi 1	experimental	Carboxymethylenecysteine
DB07849	glutathione S-transferase pi 1	experimental	S-NONYL-CYSTEINE
DB08370	glutathione S-transferase pi 1	experimental	S-(4-BROMOBENZYL)CYSTEINE
DB00443	glutathione S-transferase pi 1	approved	Betamethasone
DB01234	glutathione S-transferase pi 1	approved; investigational	Dexamethasone
DB00997	glutathione S-transferase pi 1	approved; investigational	Doxorubicin
DB01236	glutathione S-transferase pi 1	approved	Sevoflurane
DB04572	glutathione S-transferase pi 1	approved	Thiotepa
DB01229	glutathione S-transferase pi 1	approved	Paclitaxel
DB00928	glutathione S-transferase pi 1	approved; investigational	Azacitidine
DB00313	glutathione S-transferase pi 1	approved; investigational	Valproic Acid
DB00445	glutathione S-transferase pi 1	approved	Epirubicin
DB00205	glutathione S-transferase pi 1	approved	Pyrimethamine
DB01248	glutathione S-transferase pi 1	approved; investigational	Docetaxel
DB00544	glutathione S-transferase pi 1	approved	Fluorouracil
DB00291	glutathione S-transferase pi 1	approved	Chlorambucil
DB01204	glutathione S-transferase pi 1	approved; investigational	Mitoxantrone
DB00515	glutathione S-transferase pi 1	approved	Cisplatin
DB00526	glutathione S-transferase pi 1	approved; investigational	Oxaliplatin
DB00531	glutathione S-transferase pi 1	approved; investigational	Cyclophosphamide
DB00958	glutathione S-transferase pi 1	approved	Carboplatin
DB00762	glutathione S-transferase pi 1	approved; investigational	Irinotecan
DB00987	glutathione S-transferase pi 1	approved; investigational	Cytarabine
DB00694	glutathione S-transferase pi 1	approved	Daunorubicin
DB00773	glutathione S-transferase pi 1	approved	Etoposide
DB00650	glutathione S-transferase pi 1	approved	Leucovorin
DB01033	glutathione S-transferase pi 1	approved	Mercaptopurine
DB00563	glutathione S-transferase pi 1	approved	Methotrexate
DB00635	glutathione S-transferase pi 1	approved	Prednisone
DB00541	glutathione S-transferase pi 1	approved; investigational	Vincristine
DB01042	glutathione S-transferase pi 1	approved	Melphalan
DB01008	glutathione S-transferase pi 1	approved; investigational	Busulfan
DB01101	glutathione S-transferase pi 1	approved; investigational	Capecitabine

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Cross referenced IDs for GSTP1

* 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