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 PIGL
Basic gene info.Gene symbolPIGL
Gene namephosphatidylinositol glycan anchor biosynthesis, class L
SynonymsCHIME
CytomapUCSC genome browser: 17p12-p11.2
Genomic locationchr17 :16120508-16229573
Type of geneprotein-coding
RefGenesNM_004278.3,
Ensembl idENSG00000108474
DescriptionN-acetylglucosaminyl-phosphatidylinositol de-N-acetylaseN-acetylglucosaminylphosphatidylinositol deacetylasePIG-Lphosphatidylinositol glycan, class Lphosphatidylinositol-glycan biosynthesis class L protein
Modification date20141207
dbXrefs MIM : 605947
HGNC : HGNC
Ensembl : ENSG00000108474
HPRD : 12071
Vega : OTTHUMG00000059346
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIGL
BioGPS: 9487
Gene Expression Atlas: ENSG00000108474
The Human Protein Atlas: ENSG00000108474
PathwayNCI Pathway Interaction Database: PIGL
KEGG: PIGL
REACTOME: PIGL
ConsensusPathDB
Pathway Commons: PIGL
MetabolismMetaCyc: PIGL
HUMANCyc: PIGL
RegulationEnsembl's Regulation: ENSG00000108474
miRBase: chr17 :16,120,508-16,229,573
TargetScan: NM_004278
cisRED: ENSG00000108474
ContextiHOP: PIGL
cancer metabolism search in PubMed: PIGL
UCL Cancer Institute: PIGL
Assigned class in ccmGDBC

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

Mutations for PIGL
* 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
large_intestinePIGLchr171613807016138070PIGLchr171616262516162625
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 PIGL related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE706180FN1101572216264037216269224PIGL155317171616772816167890

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

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample4  1          3  
GAIN (# sample)2  1             
LOSS (# sample)2             3  
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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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

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=15)
Stat. for Synonymous SNVs
(# total SNVs=3)
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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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
chr17:16221155-16221155p.P198L1
chr17:16120548-16120548p.A3E1
chr17:16203251-16203251p.R129G1
chr17:16221169-16221169p.H203N1
chr17:16120578-16120578p.V13A1
chr17:16216915-16216915p.Y161H1
chr17:16221195-16221195p.L211L1
chr17:16120579-16120579p.V13V1
chr17:16216926-16216926p.V164V1
chr17:16221198-16221198p.N212K1

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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
# sample1  1  1 2  31   22 2
# mutation1  1  1 2  31   22 2
nonsynonymous SNV1       2  31   12 1
synonymous SNV   1  1         1  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])

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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
chr17:16120578p.E2K1
chr17:16221154p.V13A1
chr17:16120579p.V13V1
chr17:16221220p.I47I1
chr17:16120681p.A48P1
chr17:16229178p.S104C1
chr17:16120682p.H126H1
chr17:16137360p.R129G1
chr17:16203244p.V130G1
chr17:16203251p.V164V1

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 PIGL 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 PIGL

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))
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check002.gifCNV 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
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

AHSA2,ATPAF2,CENPV,CNTROB,DPH1,DRG2,KCNAB3,
LENG8,LOC338799,MAPK8IP3,MYO15B,NEURL4,NLGN2,PAN2,
PFAS,PIGL,SCX,SGSM2,TTLL3,TUBGCP6,ZSWIM7
CARF,BMS1P4,BTAF1,DNHD1,L3MBTL1,LOC100131434,LOC100272228,
LOC440944,LOC646471,MSH5,MYSM1,NKTR,PAN2,PDXDC2P,
PIGL,STAG3L3,TRIM66,CFAP70,UBE2Q2P1,WDR27,XIST

ACADVL,ALKBH6,SNHG15,CDK5RAP3,CENPV,CYP2R1,DRG2,
INCA1,PAN2,PIGL,POLR2J4,RPAIN,SNHG10,SNHG12,
SNHG3,SUV420H2,TEC,TMEM160,EMC6,TRMT1,ZSWIM7
RSRP1,CAPN10,CDK5RAP3,CHKB-CPT1B,GIPR,CLUHP3,KIFC2,
LOC100131434,LOC100272228,LOC642846,NAA40,NOXA1,NSUN5P1,NSUN5P2,
PDXDC2P,PIGL,PLEKHM1P,RHOT2,SNHG12,ZNF276,ZNF513
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

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check002.gifInteracting 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 PIGL


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



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