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 PIGU

Basic gene info.	Gene symbol	PIGU
	Gene name	phosphatidylinositol glycan anchor biosynthesis, class U
	Synonyms	CDC91L1\|GAB1
	Cytomap	UCSC genome browser: 20q11.22
	Genomic location	chr20 :33148345-33265089
	Type of gene	protein-coding
	RefGenes	NM_080476.4,
	Ensembl id	ENSG00000101464
	Description	CDC91 (cell division cycle 91, S. cerevisiae, homolog)-like 1GPI transamidase component PIG-UGPI transamidase subunitcell division cycle 91-like 1 proteincell division cycle protein 91-like 1phosphatidylinositol glycan anchor biosynthesis class U pro
	Modification date	20141207
dbXrefs	MIM : 608528
	HGNC : HGNC
	Ensembl : ENSG00000101464
	HPRD : 12250
	Vega : OTTHUMG00000032304
Protein	UniProt: Q9H490 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIGU
	BioGPS: 128869
	Gene Expression Atlas: ENSG00000101464
	The Human Protein Atlas: ENSG00000101464
Pathway	NCI Pathway Interaction Database: PIGU
	KEGG: PIGU
	REACTOME: PIGU
	ConsensusPathDB
	Pathway Commons: PIGU
Metabolism	MetaCyc: PIGU
	HUMANCyc: PIGU
Regulation	Ensembl's Regulation: ENSG00000101464
	miRBase: chr20 :33,148,345-33,265,089
	TargetScan: NM_080476
	cisRED: ENSG00000101464
Context	iHOP: PIGU
	cancer metabolism search in PubMed: PIGU
	UCL Cancer Institute: PIGU
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: PIGU
	Familial Cancer Database: PIGU

* 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	608528; gene.
Orphanet
Disease	KEGG Disease: PIGU
	MedGen: PIGU (Human Medical Genetics with Condition)
	ClinVar: PIGU
Phenotype	MGI: PIGU (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PIGU

Mutations for PIGU

* 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
central_nervous_system	PIGU	chr20	33241830	33241830	PIGU	chr20	33244289	33244289
ovary	PIGU	chr20	33162888	33162908	NCOA6	chr20	33359746	33359766
ovary	PIGU	chr20	33203667	33203687		chr20	33736874	33736894

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 PIGU 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
AA557668	PIGU	7	89	20	33148398	33148480	PIGU	86	304	20	33148477	33148696
CK823810	SLC4A4	27	156	4	72437632	72437761	PIGU	156	462	20	33185380	33185686
AW367711	PIGU	13	84	20	33158665	33158737	YARS	78	164	1	33247965	33248051
HM245395	PIGU	1	230	20	33203846	33225710	ALG5	218	616	13	37524107	37546195
HM245394	ALG5	1	272	13	37559764	37567805	PIGU	273	750	20	33162997	33176411
BM511213	SLC4A4	27	156	4	72437632	72437761	PIGU	156	420	20	33185422	33185686

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=23)	Stat. for Synonymous SNVs (# total SNVs=7)

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
chr20:33264821-33264821	p.S23R	4
chr20:33169483-33169483	p.?	2
chr20:33163023-33163023	p.C360Y	1
chr20:33231980-33231980	p.F102F	1
chr20:33173306-33173306	p.L287L	1
chr20:33222506-33222506	p.P148S	1
chr20:33169380-33169380	p.F341L	1
chr20:33232014-33232014	p.T91I	1
chr20:33173345-33173345	p.F274F	1
chr20:33225720-33225720	p.P130S	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=1

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	1		4					2	1							8	2		5
# mutation	2	1		4					2	1							8	2		5
nonsynonymous SNV	1			2					1	1							7	1		3
synonymous SNV	1	1		2					1								1	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
chr20:33169475	p.F288L	1
chr20:33225754	p.L248V	1
chr20:33173253	p.T174T	1
chr20:33231980	p.F170L	1
chr20:33173278	p.L434F	1
chr20:33232014	p.A161A	1
chr20:33148678	p.Q398Q	1
chr20:33173279	p.T159T	1
chr20:33233114	p.F386L	1
chr20:33162908	p.P148S	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 PIGU 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 PIGU

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


AHCY,ATP5E,C20orf24,AAR2,CEP250,CPNE1,DSN1, DYNLRB1,EDEM2,EIF2S2,EIF6,ERGIC3,GSS,MMP24, NFS1,PIGU,RALY,ROMO1,SCAND1,TRPC4AP,UQCC1	ALG3,C14orf1,BLOC1S4,COPZ1,DPM2,DYNLT1,EEF2KMT, H2AFZ,CERS5,PIGU,PPIL1,PSENEN,SF3B4,SPCS1, TMEM147,TMEM179B,TMEM205,TOMM6,TXN,VPS25,YIPF1

AAR2,RTFDC1,CHMP4B,CPNE1,CTNNBL1,DDX27,DPM1, DYNLRB1,EIF6,ERGIC3,GSS,NFS1,PIGU,POFUT1, PXMP4,RALY,NELFCD,TM9SF4,TP53RK,UBE2V1,UQCC1	AGPAT5,ARL6IP1,MPLKIP,DARS2,ERAL1,GSS,METTL15, MLYCD,MRPS30,MRPS5,MTIF2,NDUFA10,PIGU,PPIF, PTDSS1,RPIA,SLC35A4,SMAGP,TUFM,UNG,WARS2

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 PIGU

There's no related Drug.

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Cross referenced IDs for PIGU

* 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