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 PIGW

Basic gene info.	Gene symbol	PIGW
	Gene name	phosphatidylinositol glycan anchor biosynthesis, class W
	Synonyms	Gwt1\|HPMRS5
	Cytomap	UCSC genome browser: 17q12
	Genomic location	chr17 :34891402-34895150
	Type of gene	protein-coding
	RefGenes	NM_178517.3,
	Ensembl id	ENSG00000261300
	Description	PIG-Wphosphatidylinositol glycan, class Wphosphatidylinositol-glycan biosynthesis class W protein
	Modification date	20141207
dbXrefs	MIM : 610275
	HGNC : HGNC
	Ensembl : ENSG00000277161
	HPRD : 11432
	Vega : OTTHUMG00000188438
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIGW
	BioGPS: 284098
	Gene Expression Atlas: ENSG00000261300
	The Human Protein Atlas: ENSG00000261300
Pathway	NCI Pathway Interaction Database: PIGW
	KEGG: PIGW
	REACTOME: PIGW
	ConsensusPathDB
	Pathway Commons: PIGW
Metabolism	MetaCyc: PIGW
	HUMANCyc: PIGW
Regulation	Ensembl's Regulation: ENSG00000261300
	miRBase: chr17 :34,891,402-34,895,150
	TargetScan: NM_178517
	cisRED: ENSG00000261300
Context	iHOP: PIGW
	cancer metabolism search in PubMed: PIGW
	UCL Cancer Institute: PIGW
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: PIGW
	Familial Cancer Database: PIGW

* 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_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PIGW
	MedGen: PIGW (Human Medical Genetics with Condition)
	ClinVar: PIGW
Phenotype	MGI: PIGW (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PIGW

Mutations for PIGW

* 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 PIGW 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
AI376808	PIGW	1	263	17	34894873	34895268	POMGNT1	261	466	1	46656022	46656227
AW272407	PIGW	3	262	17	34894873	34895132	POMGNT1	260	450	1	46656022	46656212

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=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=16)

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
chr17:34893859-34893859	p.R303R	3
chr17:34893810-34893810	p.Y287C	2
chr17:34893580-34893580	p.V210V	2
chr17:34893298-34893298	p.F116L	2
chr17:34893783-34893783	p.F278C	2
chr17:34893231-34893231	p.L94*	1
chr17:34893964-34893964	p.K338N	1
chr17:34893507-34893507	p.R186K	1
chr17:34894262-34894262	p.L438I	1
chr17:34892971-34892971	p.K7K	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	1	3		3			2		1			4	2				3	1		9
# mutation	1	3		3			2		1			4	2				3	1		10
nonsynonymous SNV		3		2								2	2				2	1		7
synonymous SNV	1			1			2		1			2					1			3

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
chr17:34893298	p.F116L	2
chr17:34893408	p.K7K	1
chr17:34893963	p.E227E	1
chr17:34892971	p.L26F	1
chr17:34893433	p.R303L	1
chr17:34894104	p.Q44R	1
chr17:34893028	p.R303R	1
chr17:34893502	p.L46L	1
chr17:34894132	p.E304K	1
chr17:34893081	p.F61S	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 PIGW 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 PIGW

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


ARMC1,ATAD2,ATAD5,BRCA1,TEFM,CENPE,CKAP2L, FAM91A1,GGNBP2,GINS1,LIG3,MTDH,MYO19,PIGW, PSME3,RAD51D,SRSF1,SUZ12,TADA2A,TOP2A,WDHD1	ADSS,AMD1,ARFGAP3,B3GALNT1,CBX3,DCAF13,E2F5, LCLAT1,MAGT1,MRPL42,NRAS,NUS1,PIGW,PPHLN1, PSME3,SRSF2,TP53RK,TWISTNB,YTHDF2,ZNF207,ZWILCH

BRCA1,DDIAS,CCDC137,CSE1L,DDX10,DSN1,EFTUD2, GOSR2,LOC144486,MRM1,NOL11,PIGW,PSME3,PTRH2, PUS7,SRSF2,TMEM199,TRIM37,UTP18,UTP6,ZNHIT3	AEN,BYSL,CCDC86,DDX21,FUT4,GNL2,GTPBP4, NOP16,NOP2,ODC1,PDE12,PDF,PIGW,PMM2, PNPT1,SEH1L,SRSF2,TDG,TOMM40,TRMT6,UTP15

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 PIGW

There's no related Drug.

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Cross referenced IDs for PIGW

* 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