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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for BPGM |
Basic gene info. | Gene symbol | BPGM |
Gene name | 2,3-bisphosphoglycerate mutase | |
Synonyms | DPGM | |
Cytomap | UCSC genome browser: 7q33 | |
Genomic location | chr7 :134331530-134364567 | |
Type of gene | protein-coding | |
RefGenes | NM_001293085.1, NM_001724.4,NM_199186.2, | |
Ensembl id | ENSG00000172331 | |
Description | 2,3-bisphosphoglycerate mutase, erythrocyte2,3-bisphosphoglycerate synthase2,3-diphosphoglycerate mutaseBPG-dependent PGAMbisphosphoglycerate mutaseerythrocyte 2,3-bisphosphoglycerate mutase | |
Modification date | 20141207 | |
dbXrefs | MIM : 613896 | |
HGNC : HGNC | ||
Ensembl : ENSG00000172331 | ||
HPRD : 01961 | ||
Vega : OTTHUMG00000155380 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_BPGM | |
BioGPS: 669 | ||
Gene Expression Atlas: ENSG00000172331 | ||
The Human Protein Atlas: ENSG00000172331 | ||
Pathway | NCI Pathway Interaction Database: BPGM | |
KEGG: BPGM | ||
REACTOME: BPGM | ||
ConsensusPathDB | ||
Pathway Commons: BPGM | ||
Metabolism | MetaCyc: BPGM | |
HUMANCyc: BPGM | ||
Regulation | Ensembl's Regulation: ENSG00000172331 | |
miRBase: chr7 :134,331,530-134,364,567 | ||
TargetScan: NM_001293085 | ||
cisRED: ENSG00000172331 | ||
Context | iHOP: BPGM | |
cancer metabolism search in PubMed: BPGM | ||
UCL Cancer Institute: BPGM | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for BPGM(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: BPGM |
Familial Cancer Database: BPGM |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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: BPGM |
MedGen: BPGM (Human Medical Genetics with Condition) | |
ClinVar: BPGM | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | BPGM | chr7 | 134353288 | 134353308 | BPGM | chr7 | 134356321 | 134356341 |
pancreas | BPGM | chr7 | 134349983 | 134350003 | BPGM | chr7 | 134350407 | 134350427 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows BPGM 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 |
AI380175 | RASSF4 | 1 | 188 | 10 | 45471715 | 45471902 | BPGM | 184 | 559 | 7 | 134363981 | 134364356 | |
BQ367874 | TSC22D1 | 17 | 409 | 13 | 45008211 | 45008606 | BPGM | 398 | 560 | 7 | 134363825 | 134363987 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 1 | 1 |   |   |   |   |   |   |   |   | 1 |   |   | 1 | 1 |   |   | |||
GAIN (# sample) | 1 | 1 |   |   |   |   |   |   |   |   | 1 |   |   | 1 | 1 |   |   | |||
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=14) | (# total SNVs=4) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr7:134346845-134346845 | p.L196L | 2 |
chr7:134363772-134363772 | p.A257T | 2 |
chr7:134346605-134346605 | p.R116* | 1 |
chr7:134346768-134346768 | p.N170S | 1 |
chr7:134346628-134346628 | p.P123P | 1 |
chr7:134346791-134346791 | p.L178V | 1 |
chr7:134346262-134346262 | p.M1I | 1 |
chr7:134346662-134346662 | p.E135* | 1 |
chr7:134346797-134346797 | p.G180S | 1 |
chr7:134346316-134346316 | p.E19D | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   |   |   |   |   | 4 | 1 |   |   |   | 3 | 5 |   | 2 |
# mutation |   | 1 |   |   | 1 |   |   |   |   |   |   | 4 | 1 |   |   |   | 3 | 5 |   | 2 |
nonsynonymous SNV |   |   |   |   | 1 |   |   |   |   |   |   | 3 | 1 |   |   |   | 1 | 3 |   |   |
synonymous SNV |   | 1 |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   | 2 | 2 |   | 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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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 |
chr7:134346736 | p.E163E,BPGM | 1 |
chr7:134346744 | p.W169C,BPGM | 1 |
chr7:134346262 | p.N170S,BPGM | 1 |
chr7:134346748 | p.P175P,BPGM | 1 |
chr7:134346514 | p.G180C,BPGM | 1 |
chr7:134346766 | p.M1I,BPGM | 1 |
chr7:134346544 | p.P231H,BPGM | 1 |
chr7:134346768 | p.W85C,BPGM | 1 |
chr7:134346583 | p.L95L,BPGM | 1 |
chr7:134346784 | p.G108G,BPGM | 1 |
Other DBs for Point Mutations |
Copy 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 |
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. |
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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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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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 |
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