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 symbolPGAM4
Gene namephosphoglycerate mutase family member 4
SynonymsPGAM-B|PGAM1|PGAM3|dJ1000K24.1
CytomapUCSC genome browser: Xq13
Genomic locationchrX :77223457-77225135
Type of geneprotein-coding
RefGenesNM_001029891.2,
Ensembl idENSG00000269135
Descriptionphosphoglycerate mutase 4phosphoglycerate mutase family 3phosphoglycerate mutase processed proteinprobable phosphoglycerate mutase 4
Modification date20141207
dbXrefs MIM : 300567
HGNC : HGNC
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PGAM4
BioGPS: 441531
Gene Expression Atlas: ENSG00000269135
The Human Protein Atlas: ENSG00000269135
PathwayNCI Pathway Interaction Database: PGAM4
KEGG: PGAM4
REACTOME: PGAM4
ConsensusPathDB
Pathway Commons: PGAM4
MetabolismMetaCyc: PGAM4
HUMANCyc: PGAM4
RegulationEnsembl's Regulation: ENSG00000269135
miRBase: chrX :77,223,457-77,225,135
TargetScan: NM_001029891
cisRED: ENSG00000269135
ContextiHOP: PGAM4
cancer metabolism search in PubMed: PGAM4
UCL Cancer Institute: PGAM4
Assigned class in ccmGDBC

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Phenotypic Information for PGAM4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_GLYCOLYSIS_GLUCONEOGENESIS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PGAM4
MedGen: PGAM4 (Human Medical Genetics with Condition)
ClinVar: PGAM4
PhenotypeMGI: PGAM4 (International Mouse Phenotyping Consortium)
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.

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 PGAM4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=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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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
chr23:77224704-77224704p.D144D3
chr23:77224418-77224418p.C240R2
chr23:77224638-77224638p.F166F2
chr23:77224407-77224407p.I243M2
chr23:77224872-77224872p.N88K1
chr23:77224411-77224411p.A242D1
chr23:77225074-77225074p.R21H1
chr23:77224588-77224588p.I183S1
chr23:77224878-77224878p.R86R1
chr23:77225088-77225088p.W16C1

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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
# sample11  1 2 1  41  113 8
# mutation11  1 2 1  41  113 8
nonsynonymous SNV 1  1 1 1  3     1 5
synonymous SNV1     1    11  112 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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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
chrX:77224704p.F166F2
chrX:77224418p.D144D2
chrX:77224638p.C240R2
chrX:77224716p.L233L1
chrX:77224439p.G34S1
chrX:77224826p.N209N1
chrX:77224509p.A33A1
chrX:77224878p.E202Q1
chrX:77224532p.R21H1
chrX:77224951p.I193I1

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 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

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

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
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 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



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