Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	PIGM
	Gene name	phosphatidylinositol glycan anchor biosynthesis, class M
	Synonyms	GPI-MT-I
	Cytomap	UCSC genome browser: 1q23.2
	Genomic location	chr1 :159997461-160001783
	Type of gene	protein-coding
	RefGenes	NM_145167.2,
	Ensembl id	ENSG00000143315
	Description	DPM:GlcN-(acyl-)PI mannosyltransferaseGPI mannosyltransferase 1GPI mannosyltransferase IPIG-M mannosyltransferasedol-P-Man dependent GPI mannosyltransferasephosphatidylinositol-glycan biosynthesis class M protein
	Modification date	20141207
dbXrefs	MIM : 610273
	HGNC : HGNC
	Ensembl : ENSG00000143315
	HPRD : 15133
	Vega : OTTHUMG00000024081
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PIGM
	BioGPS: 93183
	Gene Expression Atlas: ENSG00000143315
	The Human Protein Atlas: ENSG00000143315
Pathway	NCI Pathway Interaction Database: PIGM
	KEGG: PIGM
	REACTOME: PIGM
	ConsensusPathDB
	Pathway Commons: PIGM
Metabolism	MetaCyc: PIGM
	HUMANCyc: PIGM
Regulation	Ensembl's Regulation: ENSG00000143315
	miRBase: chr1 :159,997,461-160,001,783
	TargetScan: NM_145167
	cisRED: ENSG00000143315
Context	iHOP: PIGM
	cancer metabolism search in PubMed: PIGM
	UCL Cancer Institute: PIGM
Assigned class in ccmGDB	C

Top

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

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PIGM
	MedGen: PIGM (Human Medical Genetics with Condition)
	ClinVar: PIGM
Phenotype	MGI: PIGM (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PIGM 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
AA215640	KRTCAP2	1	93	1	155144233	155144325	PIGM	91	439	1	159998972	159999323
BE843437	PIGM	31	241	1	160000558	160000768	ZBTB7C	231	430	18	45853170	45853369

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

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

Top

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=3

Top

Somatic 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)

Top

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
chr1:160000335-160000335	p.I399F	2
chr1:160000819-160000819	p.T237T	2
chr1:160001181-160001182	p.L119fs*16	1
chr1:160000512-160000512	p.L340F	1
chr1:160000857-160000857	p.R225G	1
chr1:160001229-160001229	p.S101R	1
chr1:160000536-160000536	p.T332A	1
chr1:160000905-160000905	p.Y209H	1
chr1:160001238-160001238	p.L98I	1
chr1:160000657-160000657	p.G291G	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		7			2		1			5	1	2			3	6		1
# mutation	1	1		9			2		1			5	1	2			3	6		1
nonsynonymous SNV	1	1		7					1			4					2	4
synonymous SNV				2			2					1	1	2			1	2		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

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
chr1:160000819	p.R225L	2
chr1:160000856	p.T237T	2
chr1:160001446	p.T237K	1
chr1:160000753	p.Y47H	1
chr1:160001086	p.Y35Y	1
chr1:160001449	p.R225G	1
chr1:160001137	p.F34L	1
chr1:160001510	p.Y209H	1
chr1:160000820	p.A28A	1
chr1:160001164	p.P196L	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 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]

Top

Gene Expression for PIGM

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))

Top

CNV 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

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


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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

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

Top

Pharmacological Information for PIGM

There's no related Drug.

Top

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