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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RRM2B |
Basic gene info. | Gene symbol | RRM2B |
Gene name | ribonucleotide reductase M2 B (TP53 inducible) | |
Synonyms | MTDPS8A|MTDPS8B|P53R2 | |
Cytomap | UCSC genome browser: 8q23.1 | |
Genomic location | chr8 :103216728-103251346 | |
Type of gene | protein-coding | |
RefGenes | NM_001172477.1, NM_001172478.1,NM_015713.4, | |
Ensembl id | ENSG00000048392 | |
Description | TP53-inducible ribonucleotide reductase M2 Bp53-inducible ribonucleotide reductase small subunit 2 homologp53-inducible ribonucleotide reductase small subunit 2 short form betap53-inducible ribonucleotide reductase small subunit 2-like proteinribonucl | |
Modification date | 20141207 | |
dbXrefs | MIM : 604712 | |
HGNC : HGNC | ||
Ensembl : ENSG00000048392 | ||
HPRD : 05276 | ||
Vega : OTTHUMG00000164776 | ||
Protein | UniProt: Q7LG56 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RRM2B | |
BioGPS: 50484 | ||
Gene Expression Atlas: ENSG00000048392 | ||
The Human Protein Atlas: ENSG00000048392 | ||
Pathway | NCI Pathway Interaction Database: RRM2B | |
KEGG: RRM2B | ||
REACTOME: RRM2B | ||
ConsensusPathDB | ||
Pathway Commons: RRM2B | ||
Metabolism | MetaCyc: RRM2B | |
HUMANCyc: RRM2B | ||
Regulation | Ensembl's Regulation: ENSG00000048392 | |
miRBase: chr8 :103,216,728-103,251,346 | ||
TargetScan: NM_001172477 | ||
cisRED: ENSG00000048392 | ||
Context | iHOP: RRM2B | |
cancer metabolism search in PubMed: RRM2B | ||
UCL Cancer Institute: RRM2B | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of RRM2B in cancer cell metabolism | 1. Gatto F, Miess H, Schulze A, Nielsen J (2015) Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism. Scientific reports 5. go to article |
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Phenotypic Information for RRM2B(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: RRM2B |
Familial Cancer Database: RRM2B |
* 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_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM KEGG_GLUTATHIONE_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES |
Others | |
OMIM | 604712; gene. 604712; gene. 612075; phenotype. 612075; phenotype. 613077; phenotype. 613077; phenotype. |
Orphanet | 254892; Autosomal dominant progressive external ophthalmoplegia. 254892; Autosomal dominant progressive external ophthalmoplegia. 255235; Mitochondrial DNA depletion syndrome, encephalomyopathic form with renal tubulopathy. 255235; Mitochondrial DNA depletion syndrome, encephalomyopathic form with renal tubulopathy. 298; Mitochondrial neurogastrointestinal encephalomyopathy. 298; Mitochondrial neurogastrointestinal encephalomyopathy. 329336; Adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy. 329336; Adult-onset chronic progressive external ophthalmoplegia with mitochondrial myopathy. 480; Kearns-Sayre syndrome. 480; Kearns-Sayre syndrome. |
Disease | KEGG Disease: RRM2B |
MedGen: RRM2B (Human Medical Genetics with Condition) | |
ClinVar: RRM2B | |
Phenotype | MGI: RRM2B (International Mouse Phenotyping Consortium) |
PhenomicDB: RRM2B |
Mutations for RRM2B |
* 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 RRM2B 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 |
BG999871 | ELMO1 | 1 | 284 | 7 | 36895007 | 36895295 | RRM2B | 281 | 574 | 8 | 103222283 | 103222575 |
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 |   |   |   |   | 3 |   | 2 |   |   |   |   |   | 1 | |||
GAIN (# sample) | 1 |   |   | 1 |   |   |   |   | 3 |   | 2 |   |   |   |   |   | 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=34) | (# total SNVs=2) |
(# 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 |
chr8:103220448-103220448 | p.F323L | 4 |
chr8:103244508-103244508 | p.S25G | 4 |
chr8:103251099-103251099 | p.G2C | 2 |
chr8:103220495-103220495 | p.P308S | 2 |
chr8:103231175-103231175 | p.G184V | 1 |
chr8:103238154-103238154 | p.E105K | 1 |
chr8:103225105-103225105 | p.E268K | 1 |
chr8:103244531-103244531 | p.R17T | 1 |
chr8:103236307-103236307 | p.L173L | 1 |
chr8:103238196-103238196 | p.H91Y | 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 |   |   |   | 6 |   |   | 2 |   |   |   |   | 1 | 3 | 2 |   |   | 2 | 4 |   | 7 |
# mutation |   |   |   | 4 |   |   | 2 |   |   |   |   | 1 | 3 | 2 |   |   | 2 | 4 |   | 7 |
nonsynonymous SNV |   |   |   | 3 |   |   | 1 |   |   |   |   | 1 | 3 | 2 |   |   | 1 | 3 |   | 6 |
synonymous SNV |   |   |   | 1 |   |   | 1 |   |   |   |   |   |   |   |   |   | 1 | 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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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 |
chr8:103244508 | p.S97G,RRM2B | 4 |
chr8:103237206 | p.A140S,RRM2B | 1 |
chr8:103231116 | p.L121L,RRM2B | 1 |
chr8:103244404 | p.K114N,RRM2B | 1 |
chr8:103231120 | p.K114R,RRM2B | 1 |
chr8:103244441 | p.N105S,RRM2B | 1 |
chr8:103231152 | p.L103V,RRM2B | 1 |
chr8:103244465 | p.A297E,RRM2B | 1 |
chr8:103220371 | p.K98N,RRM2B | 1 |
chr8:103236307 | p.F271L,RRM2B | 1 |
Other DBs for Point Mutations |
Copy Number for RRM2B 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 RRM2B |
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 |
ANKRD46,ARFGEF1,ATP6V1C1,AZIN1,TRIQK,CPNE3,DPY19L4, EBAG9,RMDN1,FAM91A1,KIAA0196,MTDH,RRM2B,SPAG1, STAU2,EMC2,UBE2W,UBR5,VPS13B,WWP1,ZNF252P | AHCYL2,CAB39,CUL5,EFR3A,EGLN1,FBXL17,FBXO3, FYTTD1,HCN1,IBTK,IDE,KIAA0232,KPNA1,PPTC7, RPS6KA3,RRM2B,STAU2,STRN3,SYNJ2BP,USP38,WDR47 | ||||
ATP6V1C1,ANKUB1,CPNE3,FAM91A1,GRM5,GUCA1C,IL1RL1, KHDC1L,KIAA0196,KRT1,MTDH,NBN,OR10H4,OSGIN2, PCDH9,PLGLA,RIPK2,RRM2B,STK3,TRAM1,UTS2B | PXYLP1,ALDH7A1,CCDC112,CNOT7,CPNE3,HSDL2,KCNE2, LINC01512,LRPPRC,MEST,METTL15,PLEKHG7,PRSS30P,RRM2B, SKAP2,SLC12A2,STARD7,THNSL1,UPRT,WARS2,ZBTB44 |
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 RRM2B |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Chemistry | BindingDB | Q7LG56; -. |
Chemistry | ChEMBL | CHEMBL2095215; -. |
Chemistry | BindingDB | Q7LG56; -. |
Chemistry | ChEMBL | CHEMBL2095215; -. |
Organism-specific databases | PharmGKB | PA34866; -. |
Organism-specific databases | PharmGKB | PA34866; -. |
Organism-specific databases | CTD | 50484; -. |
Organism-specific databases | CTD | 50484; -. |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00242 | ribonucleotide reductase M2 B (TP53 inducible) | approved; investigational | Cladribine |
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Cross referenced IDs for RRM2B |
* 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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