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

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 PGAM4

Basic gene info.	Gene symbol	PGAM4
	Gene name	phosphoglycerate mutase family member 4
	Synonyms	PGAM-B\|PGAM1\|PGAM3\|dJ1000K24.1
	Cytomap	UCSC genome browser: Xq13
	Genomic location	chrX :77223457-77225135
	Type of gene	protein-coding
	RefGenes	NM_001029891.2,
	Ensembl id	ENSG00000269135
	Description	phosphoglycerate mutase 4phosphoglycerate mutase family 3phosphoglycerate mutase processed proteinprobable phosphoglycerate mutase 4
	Modification date	20141207
dbXrefs	MIM : 300567
	HGNC : HGNC
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PGAM4
	BioGPS: 441531
	Gene Expression Atlas: ENSG00000269135
	The Human Protein Atlas: ENSG00000269135
Pathway	NCI Pathway Interaction Database: PGAM4
	KEGG: PGAM4
	REACTOME: PGAM4
	ConsensusPathDB
	Pathway Commons: PGAM4
Metabolism	MetaCyc: PGAM4
	HUMANCyc: PGAM4
Regulation	Ensembl's Regulation: ENSG00000269135
	miRBase: chrX :77,223,457-77,225,135
	TargetScan: NM_001029891
	cisRED: ENSG00000269135
Context	iHOP: PGAM4
	cancer metabolism search in PubMed: PGAM4
	UCL Cancer Institute: PGAM4
Assigned class in ccmGDB	C

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Phenotypic Information for PGAM4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PGAM4
	Familial Cancer Database: PGAM4

* 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
KEGG_GLYCOLYSIS_GLUCONEOGENESIS

Others
OMIM
Orphanet
Disease	KEGG Disease: PGAM4
	MedGen: PGAM4 (Human Medical Genetics with Condition)
	ClinVar: PGAM4
Phenotype	MGI: PGAM4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PGAM4

Mutations for PGAM4

* 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 PGAM4 related fusion information.

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

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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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

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=24)	Stat. for Synonymous SNVs (# total SNVs=8)

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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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
chr23:77224704-77224704	p.D144D	3
chr23:77224638-77224638	p.F166F	2
chr23:77224407-77224407	p.I243M	2
chr23:77224418-77224418	p.C240R	2
chr23:77224951-77224951	p.R62I	1
chr23:77224481-77224481	p.E219*	1
chr23:77224622-77224622	p.V172F	1
chr23:77224968-77224968	p.L56L	1
chr23:77224485-77224485	p.V217V	1
chr23:77224990-77224990	p.G49V	1

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

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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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
chrX:77224638	p.F166F	2
chrX:77224704	p.D144D	2
chrX:77224418	p.C240R	2
chrX:77224579	p.K176K	1
chrX:77225016	p.R140R	1
chrX:77224588	p.A104T	1
chrX:77225036	p.R86R	1
chrX:77224607	p.A245D	1
chrX:77225037	p.R62I	1
chrX:77224608	p.I243M	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 PGAM4 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 PGAM4

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))

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CNV 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

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


C10orf12,CHUK,CNOT1,DDX21,EIF2S1,EIF4G1,ERO1L, FAM45B,HSPA8,IARS,IDE,LDHA,LIMS1,LOC284441, MMS19,NOLC1,PGAM1,PGAM4,PGK1,PKM,RRAGC	ADAMTS2,ANXA2,ANXA2P1,ANXA2P2,CTNNA1,EXT2,FKBP9, GNA12,GPR153,ICMT,KDELR3,LASP1,PGAM1,PGAM4, PGD,PNMA1,PXDN,SAE1,SURF4,TMEM104,UNC13B

ACTR3BP2,HSFX1,LCE2B,LOC653545,LOC728410,OR6N2,OR8B3, PGAM4,POTEE,PPIAL4B,PRAMEF17,PRAMEF3,RBMY1B,RPL13AP20, RPL13AP6,RPL21,RPS26P11,RPSAP9,SNORA38,SNORD104,SNORD16, SNORD35B,SNORD58C,SNORD62A,SNORD76,SNORD88B,SNORD88C,TPI1P3	ASS1,CASP5,COX17,DYNLT1,ERP44,NEDD8,PGAM1, PGAM4,POMP,PPP1R7,PSMA3,PSMB3,PSMC1,PSMC4, SEC61B,SEC61G,SHFM1,SLC35B1,SOD1,SUGT1,TSPAN8

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

: Open all plots for all cancer types

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Interacting 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 PGAM4

There's no related Drug.

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Cross referenced IDs for PGAM4

* 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