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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for POLR3B |
Basic gene info. | Gene symbol | POLR3B |
Gene name | polymerase (RNA) III (DNA directed) polypeptide B | |
Synonyms | C128|HLD8|INMAP|RPC2 | |
Cytomap | UCSC genome browser: 12q23.3 | |
Genomic location | chr12 :106751435-106903976 | |
Type of gene | protein-coding | |
RefGenes | NM_001160708.1, NM_018082.5, | |
Ensembl id | ENSG00000013503 | |
Description | DNA-directed RNA polymerase III 127.6 kDa polypeptideDNA-directed RNA polymerase III subunit BDNA-directed RNA polymerase III subunit RPC2RNA polymerase III subunit C2interphase nucleus and mitotic apparatus associated protein | |
Modification date | 20141219 | |
dbXrefs | MIM : 614366 | |
HGNC : HGNC | ||
Ensembl : ENSG00000013503 | ||
HPRD : 11447 | ||
Vega : OTTHUMG00000170077 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_POLR3B | |
BioGPS: 55703 | ||
Gene Expression Atlas: ENSG00000013503 | ||
The Human Protein Atlas: ENSG00000013503 | ||
Pathway | NCI Pathway Interaction Database: POLR3B | |
KEGG: POLR3B | ||
REACTOME: POLR3B | ||
ConsensusPathDB | ||
Pathway Commons: POLR3B | ||
Metabolism | MetaCyc: POLR3B | |
HUMANCyc: POLR3B | ||
Regulation | Ensembl's Regulation: ENSG00000013503 | |
miRBase: chr12 :106,751,435-106,903,976 | ||
TargetScan: NM_001160708 | ||
cisRED: ENSG00000013503 | ||
Context | iHOP: POLR3B | |
cancer metabolism search in PubMed: POLR3B | ||
UCL Cancer Institute: POLR3B | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for POLR3B(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: POLR3B |
Familial Cancer Database: POLR3B |
* This gene is included in those cancer gene databases. |
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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 |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: POLR3B |
MedGen: POLR3B (Human Medical Genetics with Condition) | |
ClinVar: POLR3B | |
Phenotype | MGI: POLR3B (International Mouse Phenotyping Consortium) |
PhenomicDB: POLR3B |
Mutations for POLR3B |
* 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 | POLR3B | chr12 | 106887700 | 106887720 | POLR3B | chr12 | 106883358 | 106883378 |
pancreas | POLR3B | chr12 | 106865379 | 106865399 | chr12 | 106676895 | 106676915 |
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 POLR3B 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 |
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 |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 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=94) | (# total SNVs=25) |
(# total SNVs=1) | (# 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 |
chr12:106820975-106820975 | p.L368F | 12 |
chr12:106820987-106820987 | p.L372F | 4 |
chr12:106850924-106850924 | p.R768C | 3 |
chr12:106850985-106850985 | p.D788V | 3 |
chr12:106890685-106890685 | p.S991S | 2 |
chr12:106824234-106824234 | p.D483N | 2 |
chr12:106851060-106851060 | p.G813V | 2 |
chr12:106772119-106772119 | p.V191M | 2 |
chr12:106903291-106903291 | p.I1122I | 2 |
chr12:106838340-106838340 | p.Y685Y | 2 |
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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 | 2 | 2 | 2 | 16 | 1 |   | 3 |   | 2 | 1 | 1 | 18 | 5 | 2 |   |   | 17 | 13 | 1 | 13 |
# mutation | 2 | 2 | 2 | 17 | 1 |   | 3 |   | 2 | 1 | 1 | 19 | 5 | 2 |   |   | 18 | 13 | 1 | 15 |
nonsynonymous SNV | 1 | 2 | 2 | 13 | 1 |   | 2 |   | 2 | 1 | 1 | 17 | 1 | 1 |   |   | 14 | 8 | 1 | 13 |
synonymous SNV | 1 |   |   | 4 |   |   | 1 |   |   |   |   | 2 | 4 | 1 |   |   | 4 | 5 |   | 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 |
chr12:106890685 | p.S933S,POLR3B | 3 |
chr12:106763072 | p.G25W,POLR3B | 2 |
chr12:106804719 | p.R303Q,POLR3B | 2 |
chr12:106851069 | p.R164Q,POLR3B | 1 |
chr12:106903245 | p.R370G,POLR3B | 1 |
chr12:106763069 | p.A507A,POLR3B | 1 |
chr12:106824083 | p.N716H,POLR3B | 1 |
chr12:106890582 | p.G908G,POLR3B | 1 |
chr12:106772118 | p.G38C | 1 |
chr12:106826181 | p.R988H,POLR3B | 1 |
Other DBs for Point Mutations |
Copy Number for POLR3B 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 POLR3B |
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 |
ATP2A2,BRAP,PARPBP,DENR,DHX9,FBXO21,GTF2H3, METAP2,MRPL42,NAA25,NUP37,POLR3B,PPP1CC,PTPN11, PWP1,SART3,SBNO1,SCYL2,TDG,TMPO,UTP20 | BRCC3,ASUN,COA7,DHX9,EARS2,EPRS,IARS, LARS,NLN,POLR3B,RPA1,SDAD1,STT3B,TEX2, TFCP2,TSR1,TSTD2,USP7,VPRBP,WDR12,WDR3 |
AACS,ATP2A2,ATP5B,BRAP,CAND1,CNOT2,CS, DDX54,FBXO21,GCN1L1,GTF2H3,METAP2,NAA25,POLR3B, PPP1CC,SART3,SBNO1,SETD8,SHMT2,SLC25A3,UNG | AGPS,AQR,DARS2,EFTUD2,G3BP1,GPHN,HSPA9, FOCAD,LARS2,LARS,LRPPRC,MLEC,NARS,NEK4, NUP160,POLR1B,POLR3B,PTDSS1,SKIV2L2,SRPK1,STT3B |
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 POLR3B |
There's no related Drug. |
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Cross referenced IDs for POLR3B |
* 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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