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 PIGK
Basic gene info.Gene symbolPIGK
Gene namephosphatidylinositol glycan anchor biosynthesis, class K
SynonymsGPI8
CytomapUCSC genome browser: 1p31.1
Genomic locationchr1 :77554666-77685132
Type of geneprotein-coding
RefGenesNM_005482.2,
Ensembl idENSG00000142892
DescriptionGPI transamidase subunitGPI-anchor transamidaseGPI8 homologPIG-Kphosphatidylinositol glycan, class Kphosphatidylinositol-glycan biosynthesis class K protein
Modification date20141207
dbXrefs MIM : 605087
HGNC : HGNC
Ensembl : ENSG00000142892
HPRD : 05474
Vega : OTTHUMG00000009686
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIGK
BioGPS: 10026
Gene Expression Atlas: ENSG00000142892
The Human Protein Atlas: ENSG00000142892
PathwayNCI Pathway Interaction Database: PIGK
KEGG: PIGK
REACTOME: PIGK
ConsensusPathDB
Pathway Commons: PIGK
MetabolismMetaCyc: PIGK
HUMANCyc: PIGK
RegulationEnsembl's Regulation: ENSG00000142892
miRBase: chr1 :77,554,666-77,685,132
TargetScan: NM_005482
cisRED: ENSG00000142892
ContextiHOP: PIGK
cancer metabolism search in PubMed: PIGK
UCL Cancer Institute: PIGK
Assigned class in ccmGDBC

Top
Phenotypic Information for PIGK(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PIGK
Familial Cancer Database: PIGK
* 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: PIGK
MedGen: PIGK (Human Medical Genetics with Condition)
ClinVar: PIGK
PhenotypeMGI: PIGK (International Mouse Phenotyping Consortium)
PhenomicDB: PIGK

Mutations for PIGK
* 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

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPIGKchr17759071577590735chr17753363877533658
ovaryPIGKchr17766161677661636AK5chr17775268677752706
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PIGK related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CB243604PIGK110317759529577595396KIF21A89415123972615439726810

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1       2   11  1
GAIN (# sample)1       2    1  1
LOSS (# sample)            1    
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)

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=5

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=43)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr1:77620288-77620288p.S278G3
chr1:77627341-77627341p.R214*3
chr1:77620260-77620260p.R287H3
chr1:77627004-77627004p.A263A2
chr1:77627340-77627340p.R214Q2
chr1:77676161-77676161p.Q36R2
chr1:77632504-77632504p.E129D2
chr1:77620261-77620261p.R287C1
chr1:77634963-77634963p.V119V1
chr1:77627318-77627318p.M221I1

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
# sample2 18  4 1  312  62 9
# mutation2 18  4 1  312  62 8
nonsynonymous SNV2  6  3 1  211  51 7
synonymous SNV  12  1    1 1  11 1
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
chr1:77632504p.E129D2
chr1:77627290p.D333G1
chr1:77632457p.M211I1
chr1:77588033p.R54Q1
chr1:77672403p.E311Q1
chr1:77627328p.A209S1
chr1:77632477p.E35E1
chr1:77620189p.F303F1
chr1:77676163p.Q207K1
chr1:77627338p.L7V1

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 PIGK 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 PIGK

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

AK5,ANKRD13C,ATP7A,TMEM245,CCPG1,CPEB3,FAM73A,
FPGT,GNG12,ESRG,EFCAB14,MIER1,MYNN,PIGK,
PJA2,RAB33B,SPATA6,STAM2,TCP11L2,USP33,ZZZ3
CASC4,CTSO,ERLEC1,FAM3C,HIAT1,LAMP2,MIER1,
PIGK,RAB11A,RAB14,SCOC,SELT,SPTLC1,TM9SF3,
TMED7,TMX1,TRAM1,TWF1,TWSG1,UBLCP1,ZMPSTE24

ABCD3,AGL,ATG4C,BCAS2,CEPT1,DBT,DR1,
FPGT,HIAT1,PIGK,RAP1A,RNF11,SCP2,SEP15,
SH3GLB1,SIKE1,STXBP3,TMED5,TMEM167B,USP33,ZZZ3
TMEM237,NADK2,CDC73,COPS8,CWC27,DARS,DYNC1LI1,
HIAT1,KIAA1586,NBN,PIGK,PRTFDC1,RAB28,RPAP3,
RPRD1A,SMARCE1,SSB,STYX,SYPL1,UTP11L,YBX1
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 PIGK


There's no related Drug.
Top
Cross referenced IDs for PIGK
* 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