Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 PIGM
Basic gene info.Gene symbolPIGM
Gene namephosphatidylinositol glycan anchor biosynthesis, class M
SynonymsGPI-MT-I
CytomapUCSC genome browser: 1q23.2
Genomic locationchr1 :159997461-160001783
Type of geneprotein-coding
RefGenesNM_145167.2,
Ensembl idENSG00000143315
DescriptionDPM:GlcN-(acyl-)PI mannosyltransferaseGPI mannosyltransferase 1GPI mannosyltransferase IPIG-M mannosyltransferasedol-P-Man dependent GPI mannosyltransferasephosphatidylinositol-glycan biosynthesis class M protein
Modification date20141207
dbXrefs MIM : 610273
HGNC : HGNC
Ensembl : ENSG00000143315
HPRD : 15133
Vega : OTTHUMG00000024081
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PIGM
BioGPS: 93183
Gene Expression Atlas: ENSG00000143315
The Human Protein Atlas: ENSG00000143315
PathwayNCI Pathway Interaction Database: PIGM
KEGG: PIGM
REACTOME: PIGM
ConsensusPathDB
Pathway Commons: PIGM
MetabolismMetaCyc: PIGM
HUMANCyc: PIGM
RegulationEnsembl's Regulation: ENSG00000143315
miRBase: chr1 :159,997,461-160,001,783
TargetScan: NM_145167
cisRED: ENSG00000143315
ContextiHOP: PIGM
cancer metabolism search in PubMed: PIGM
UCL Cancer Institute: PIGM
Assigned class in ccmGDBC

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

Mutations for PIGM
* 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 PIGM related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA215640KRTCAP21931155144233155144325PIGM914391159998972159999323
BE843437PIGM312411160000558160000768ZBTB7C231430184585317045853369

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
There's no copy number variation information in COSMIC data for this gene.

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=19)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=2)

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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
chr1:160000335-160000335p.I399F2
chr1:160000819-160000819p.T237T2
chr1:160000712-160000712p.P273R1
chr1:160001067-160001067p.L155L1
chr1:160000288-160000290p.E414delE1
chr1:160001425-160001425p.Y35Y1
chr1:160000753-160000753p.F259F1
chr1:160001078-160001078p.A151V1
chr1:160001428-160001428p.F34L1
chr1:160000788-160000788p.E248Q1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 7  2 1  512  36 1
# mutation11 9  2 1  512  36 1
nonsynonymous SNV11 7    1  4    24  
synonymous SNV   2  2    112  12 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
chr1:160000819p.T237T2
chr1:160000856p.R225L2
chr1:160000905p.L394L1
chr1:160001238p.S148S1
chr1:160000350p.G291G1
chr1:160000943p.W131C1
chr1:160001252p.F275L1
chr1:160000657p.R122R1
chr1:160000969p.Y274C1
chr1:160001391p.L115P1

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 PIGM 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 PIGM

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

ANGEL2,ATF6,BLZF1,TRMT1L,C1orf27,SUCO,CDC73,
COPA,DARS2,EDEM3,GGPS1,CERS2,NCSTN,NSL1,
PEX19,PIGM,SDHC,SLC25A44,TADA1,TMCO1,TROVE2
AP1AR,SUCO,SMIM15,INIP,CNOT6,CMTR2,GALNT4,
GOLPH3L,LZTFL1,NXT2,PIGM,POT1,PRRC1,RBBP9,
PTBP3,SS18,TMEM168,TMEM33,TTC30A,VPS4B,ZNF260

ANGEL2,BCL9,DIEXF,TRMT1L,DCAF8,GPR89A,HEATR1,
KLHL12,METTL13,MTR,PIGM,POGK,POLR3C,RAB3GAP2,
SETDB1,STX6,TDRKH,UBE2Q1,UBQLN4,VANGL2,ZNF687
ALKBH8,CCDC113,CLCC1,DENND4A,DPY19L3,FAM122A,HEATR1,
IL6ST,KIAA0754,LDLRAD3,LOC643837,MAN1A2,NAA25,PGM2L1,
PIGM,RPGRIP1L,SDAD1,TRIM44,TSR1,WDR36,XPO4
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 PIGM


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