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 BPGM
Basic gene info.Gene symbolBPGM
Gene name2,3-bisphosphoglycerate mutase
SynonymsDPGM
CytomapUCSC genome browser: 7q33
Genomic locationchr7 :134331530-134364567
Type of geneprotein-coding
RefGenesNM_001293085.1,
NM_001724.4,NM_199186.2,
Ensembl idENSG00000172331
Description2,3-bisphosphoglycerate mutase, erythrocyte2,3-bisphosphoglycerate synthase2,3-diphosphoglycerate mutaseBPG-dependent PGAMbisphosphoglycerate mutaseerythrocyte 2,3-bisphosphoglycerate mutase
Modification date20141207
dbXrefs MIM : 613896
HGNC : HGNC
Ensembl : ENSG00000172331
HPRD : 01961
Vega : OTTHUMG00000155380
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BPGM
BioGPS: 669
Gene Expression Atlas: ENSG00000172331
The Human Protein Atlas: ENSG00000172331
PathwayNCI Pathway Interaction Database: BPGM
KEGG: BPGM
REACTOME: BPGM
ConsensusPathDB
Pathway Commons: BPGM
MetabolismMetaCyc: BPGM
HUMANCyc: BPGM
RegulationEnsembl's Regulation: ENSG00000172331
miRBase: chr7 :134,331,530-134,364,567
TargetScan: NM_001293085
cisRED: ENSG00000172331
ContextiHOP: BPGM
cancer metabolism search in PubMed: BPGM
UCL Cancer Institute: BPGM
Assigned class in ccmGDBC

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

Mutations for BPGM
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryBPGMchr7134353288134353308BPGMchr7134356321134356341
pancreasBPGMchr7134349983134350003BPGMchr7134350407134350427
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows BPGM related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI380175RASSF41188104547171545471902BPGM1845597134363981134364356
BQ367874TSC22D117409134500821145008606BPGM3985607134363825134363987

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample11        1  11  
GAIN (# sample)11        1  11  
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=14)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr7:134346845-134346845p.L196L2
chr7:134363772-134363772p.A257T2
chr7:134346371-134346371p.A38T1
chr7:134346694-134346694p.C145C1
chr7:134346399-134346399p.A47V1
chr7:134346715-134346715p.L152L1
chr7:134363673-134363673p.E224K1
chr7:134346437-134346437p.L60F1
chr7:134346716-134346716p.P153S1
chr7:134363695-134363695p.P231H1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1  1      41   35 2
# mutation 1  1      41   35 2
nonsynonymous SNV    1      31   13  
synonymous SNV 1         1    22 2
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
chr7:134346544p.G108G,BPGM1
chr7:134346768p.P123P,BPGM1
chr7:134346583p.R140W,BPGM1
chr7:134346784p.C145C,BPGM1
chr7:134346628p.S155L,BPGM1
chr7:134346797p.S155S,BPGM1
chr7:134346677p.K159K,BPGM1
chr7:134363695p.L162P,BPGM1
chr7:134346694p.E163E,BPGM1
chr7:134346723p.W169C,BPGM1

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 BPGM 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 BPGM

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

AGK,BPGM,C7orf49,C7orf60,CALD1,CBX3,CNOT4,
CYCS,DUS4L,LOC401397,LRGUK,LSM5,LUZP6,MTERF1,
NRBF2,NUPL2,C7orf73,RHEB,SLC35B4,TMEM209,TMEM60
AKTIP,ANXA7,BPGM,CAPZA2,COPS4,COPS8,DSCR4,
FEZ2,KCMF1,KIAA1279,LOC401397,MYL12A,NDUFA5,PCMT1,
PRPS1,PSMC6,RAB12,TIMM17A,TM6SF1,TMEM70,VBP1

A4GALT,AXL,BICC1,BPGM,CALU,CAV1,CAV2,
CDK14,CTSK,NR2F1-AS1,FRMD6,IGFBP6,INHBA,ISLR,
ITGB1,LRRC17,PDGFC,RPSAP52,SERPINE1,SNAI2,TIMP2
BPGM,ARL14EP,C1orf123,BRK1,C4orf27,CCDC53,COMMD6,
CRYZL1,MORF4L1,MYL6,PAIP2,PCMT1,PKIG,PPT1,
RAP1A,SEPT10,SNAPIN,SNX3,TTC33,UQCRB,UROD
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 BPGM


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