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 PGAM1
Basic gene info.Gene symbolPGAM1
Gene namephosphoglycerate mutase 1 (brain)
SynonymsHEL-S-35|PGAM-B|PGAMA
CytomapUCSC genome browser: 10q25.3
Genomic locationchr10 :99186026-99193198
Type of geneprotein-coding
RefGenesNM_002629.2,
Ensembl idENSG00000171314
DescriptionBPG-dependent PGAM 1epididymis secretory protein Li 35phosphoglycerate mutase 1phosphoglycerate mutase A, nonmuscle formphosphoglycerate mutase isozyme B
Modification date20141207
dbXrefs MIM : 172250
HGNC : HGNC
Ensembl : ENSG00000171314
HPRD : 01392
Vega : OTTHUMG00000018846
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PGAM1
BioGPS: 5223
Gene Expression Atlas: ENSG00000171314
The Human Protein Atlas: ENSG00000171314
PathwayNCI Pathway Interaction Database: PGAM1
KEGG: PGAM1
REACTOME: PGAM1
ConsensusPathDB
Pathway Commons: PGAM1
MetabolismMetaCyc: PGAM1
HUMANCyc: PGAM1
RegulationEnsembl's Regulation: ENSG00000171314
miRBase: chr10 :99,186,026-99,193,198
TargetScan: NM_002629
cisRED: ENSG00000171314
ContextiHOP: PGAM1
cancer metabolism search in PubMed: PGAM1
UCL Cancer Institute: PGAM1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PGAM1 in cancer cell metabolism1. Obre E, Rossignol R (2015) Emerging concepts in bioenergetics and cancer research: metabolic flexibility, coupling, symbiosis, switch, oxidative tumors, metabolic remodeling, signaling and bioenergetic therapy. Int J Biochem Cell Biol 59: 167-181. doi: 10.1016/j.biocel.2014.12.008. go to article
2. Jiang X, Sun Q, Li H, Li K, Ren X (2014) The role of phosphoglycerate mutase 1 in tumor aerobic glycolysis and its potential therapeutic implications. Int J Cancer 135: 1991-1996. doi: 10.1002/ijc.28637. go to article
3. Stine ZE, Dang CV (2013) Stress eating and tuning out: cancer cells re-wire metabolism to counter stress. Crit Rev Biochem Mol Biol 48: 609-619. doi: 10.3109/10409238.2013.844093. pmid: 4063414. go to article
4. Hitosugi T, Zhou L, Fan J, Elf S, Zhang L, et al. (2013) Tyr26 phosphorylation of PGAM1 provides a metabolic advantage to tumours by stabilizing the active conformation. Nat Commun 4: 1790. doi: 10.1038/ncomms2759. pmid: 3648882. go to article
5. Chaneton B, Gottlieb E (2012) PGAMgnam style: a glycolytic switch controls biosynthesis. Cancer Cell 22: 565-566. doi: 10.1016/j.ccr.2012.10.014. go to article

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Phenotypic Information for PGAM1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PGAM1
Familial Cancer Database: PGAM1
* 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
BIOCARTA_GLYCOLYSIS_PATHWAY
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PGAM1
MedGen: PGAM1 (Human Medical Genetics with Condition)
ClinVar: PGAM1
PhenotypeMGI: PGAM1 (International Mouse Phenotyping Consortium)
PhenomicDB: PGAM1

Mutations for PGAM1
* 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 PGAM1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK125057SMAD211430184545311645454544PGAM114313139109918603799193197
CN393630ATP7A163X7722363577223697PGAM164581109919226299192779

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=9)
Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr10:99192235-99192235p.R240H2
chr10:99190257-99190257p.L87L1
chr10:99190263-99190263p.E89E1
chr10:99190264-99190264p.R90W1
chr10:99190719-99190719p.R141M1
chr10:99190736-99190736p.E147K1
chr10:99190742-99190742p.Q149E1
chr10:99190894-99190894p.?1
chr10:99192182-99192182p.K222N1
chr10:99186086-99186086p.L8V1

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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 14    1  2       4
# mutation1 13    1  2       4
nonsynonymous SNV1 13    1  1       3
synonymous SNV           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
chr10:99192235p.R240H2
chr10:99190253p.L8V1
chr10:99190257p.A63V1
chr10:99190263p.R86H1
chr10:99190264p.L87L1
chr10:99190719p.E89E1
chr10:99190736p.R90W1
chr10:99190742p.R141M1
chr10:99190814p.E147K1
chr10:99186071p.Q149E1

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 PGAM1 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 PGAM1

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

ACTR1A,ARPC2,AVEN,BNIP3,ENO1,GAPDH,GLRX3,
GOT1,GPI,GSTO1,LDHA,PGAM1,PGAM4,PGK1,
PKM,PSMB2,RAN,SLC16A3,TPI1,TUBA1C,USMG5
ANXA2,ANXA2P1,ANXA2P2,ATP1B3,ATP6V0E1,EMC7,SLC35F6,
CD63,CRYL1,DOLK,DYNLL1,FUCA2,IFNGR2,MSRA,
NUDT5,PGAM1,PRDX4,RHOA,SNX11,UBE2L3,VKORC1

ALDOA,ATP5A1,ATP5B,TIMM21,MCU,EIF4A1,EIF5A,
EIF5AL1,ENO1,GAPDH,LDHA,P4HA1,PFKP,PGAM1,
PKM,PLEK2,SFXN1,SLC16A3,TPI1,TUBA1B,TYMS
ATP6V1E1,SLIRP,DYNLT1,LSM3,MRPL20,NEDD8,PGAM1,
POMP,PSMA1,PSMA2,PSMA3,PSMA6,PSMA7,PSMB1,
PSMB5,PSMB6,PSMC2,PSMC3,PSMC4,PSMD13,RHOA
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 PGAM1


There's no related Drug.
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Cross referenced IDs for PGAM1
* 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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