Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 PIGA
Basic gene info.Gene symbolPIGA
Gene namephosphatidylinositol glycan anchor biosynthesis, class A
SynonymsGPI3|MCAHS2|PIG-A|PNH1
CytomapUCSC genome browser: Xp22.1
Genomic locationchrX :15337572-15353676
Type of geneprotein-coding
RefGenesNM_002641.3,
NM_020473.3,NR_033835.1,NR_033836.1,NM_020472.1,
Ensembl idENSG00000165195
DescriptionGLCNAC-PI synthesis proteinGPI anchor biosynthesisclass A GlcNAc-inositol phospholipid assembly proteinphosphatidylinositol N-acetylglucosaminyltransferase subunit Aphosphatidylinositol-glycan biosynthesis, class A protein
Modification date20141207
dbXrefs MIM : 311770
HGNC : HGNC
Ensembl : ENSG00000165195
HPRD : 02410
Vega : OTTHUMG00000021174
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIGA
BioGPS: 5277
Gene Expression Atlas: ENSG00000165195
The Human Protein Atlas: ENSG00000165195
PathwayNCI Pathway Interaction Database: PIGA
KEGG: PIGA
REACTOME: PIGA
ConsensusPathDB
Pathway Commons: PIGA
MetabolismMetaCyc: PIGA
HUMANCyc: PIGA
RegulationEnsembl's Regulation: ENSG00000165195
miRBase: chrX :15,337,572-15,353,676
TargetScan: NM_002641
cisRED: ENSG00000165195
ContextiHOP: PIGA
cancer metabolism search in PubMed: PIGA
UCL Cancer Institute: PIGA
Assigned class in ccmGDBC

Top
Phenotypic Information for PIGA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PIGA
Familial Cancer Database: PIGA
* 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_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PIGA
MedGen: PIGA (Human Medical Genetics with Condition)
ClinVar: PIGA
PhenotypeMGI: PIGA (International Mouse Phenotyping Consortium)
PhenomicDB: PIGA

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

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PIGA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

Top
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=2

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr23:15349629-15349629p.A142T2
chr23:15349630-15349630p.H141H2
chr23:15349444-15349444p.V203V1
chr23:15349690-15349690p.R121R1
chr23:15339736-15339736p.S449S1
chr23:15349932-15349932p.F41V1
chr23:15342939-15342939p.I346V1
chr23:15349466-15349466p.A196E1
chr23:15349735-15349735p.L106L1
chr23:15339751-15339751p.W444C1

Top
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
# sample1214  3 2  5 1 132 10
# mutation1214  3 2  5 1 142 10
nonsynonymous SNV 212  1    4 1 131 8
synonymous SNV1  2  2 2  1    11 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])

Top
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
chrX:15344163p.A142T2
chrX:15349629p.D7N,PIGA2
chrX:15349660p.D222D,PIGA1
chrX:15350018p.T213I1
chrX:15339751p.S51N1
chrX:15344151p.S215S,PIGA1
chrX:15349690p.V203V1
chrX:15339761p.M37T1
chrX:15349714p.W210C,PIGA1
chrX:15339870p.C183Y1

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 PIGA 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]

Top
Gene Expression for PIGA

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

ARSD,B4GALNT1,CCT5,DCLRE1B,DYRK2,FANCB,GJA10,
HCCS,KPNA4,ME1,METTL7B,MOSPD2,NUP160,OR9K2,
PGM3,PIGA,PIR,POLA1,RAB9A,TRIM55,TXLNG
ABHD13,AEBP2,B3GNT2,BIRC2,DENND6A,MARCH7,MYNN,
PGGT1B,PIGA,RBM12,RBMXL1,RYBP,SRSF10,STXBP3,
SYNCRIP,TMEM161B,TWISTNB,WEE1,ZNF267,ZBTB21,ZNF800

ATP6AP2,ELK1,FANCB,FTSJ1,HCCS,MBTPS2,MORF4L2,
MSL3,JADE3,PIGA,POLA1,PRPS2,RAP2C,RLIM,
RP2,SCML1,SLC35A2,SMS,TAB3,VBP1,ZNF674
ALG6,ARPC5L,BZW1,CHUK,DHX15,FAM91A1,MAP2K4,
NFE2L2,PDE12,PGGT1B,PIGA,PPP1R15B,PRPF40A,PSME3,
SCYL2,SGPP1,SPTY2D1,TDG,TMEM167A,YWHAZ,ZNF207
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for PIGA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB03014phosphatidylinositol glycan anchor biosynthesis, class AexperimentalHeme


Top
Cross referenced IDs for PIGA
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas