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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for POLR2J |
Basic gene info. | Gene symbol | POLR2J |
Gene name | polymerase (RNA) II (DNA directed) polypeptide J, 13.3kDa | |
Synonyms | POLR2J1|RPB11|RPB11A|RPB11m|hRPB14 | |
Cytomap | UCSC genome browser: 7q22.1 | |
Genomic location | chr7 :102113547-102119381 | |
Type of gene | protein-coding | |
RefGenes | NM_006234.4, | |
Ensembl id | ENSG00000005075 | |
Description | DNA-directed RNA polymerase II subunit J-1DNA-directed RNA polymerase II subunit RPB11-aRNA polymerase II 13.3 kDa subunitRNA polymerase II subunit B11-a | |
Modification date | 20141207 | |
dbXrefs | MIM : 604150 | |
HGNC : HGNC | ||
Ensembl : ENSG00000005075 | ||
HPRD : 16038 | ||
Vega : OTTHUMG00000150387 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_POLR2J | |
BioGPS: 5439 | ||
Gene Expression Atlas: ENSG00000005075 | ||
The Human Protein Atlas: ENSG00000005075 | ||
Pathway | NCI Pathway Interaction Database: POLR2J | |
KEGG: POLR2J | ||
REACTOME: POLR2J | ||
ConsensusPathDB | ||
Pathway Commons: POLR2J | ||
Metabolism | MetaCyc: POLR2J | |
HUMANCyc: POLR2J | ||
Regulation | Ensembl's Regulation: ENSG00000005075 | |
miRBase: chr7 :102,113,547-102,119,381 | ||
TargetScan: NM_006234 | ||
cisRED: ENSG00000005075 | ||
Context | iHOP: POLR2J | |
cancer metabolism search in PubMed: POLR2J | ||
UCL Cancer Institute: POLR2J | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for POLR2J(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: POLR2J |
Familial Cancer Database: POLR2J |
* 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: POLR2J |
MedGen: POLR2J (Human Medical Genetics with Condition) | |
ClinVar: POLR2J | |
Phenotype | MGI: POLR2J (International Mouse Phenotyping Consortium) |
PhenomicDB: POLR2J |
Mutations for POLR2J |
* 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 POLR2J 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 |
BI049495 | POLR2J | 1 | 140 | 7 | 102116649 | 102119325 | STARD13 | 136 | 227 | 13 | 34003915 | 34004006 | |
AI202736 | POLR2J | 6 | 74 | 7 | 102113910 | 102113978 | DLGAP4 | 64 | 606 | 20 | 35125134 | 35128721 |
Other DBs for Structural Variants |
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Copy 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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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=4) | (# total SNVs=1) |
(# 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 |
chr7:102119254-102119256 | p.? | 3 |
chr7:102119268-102119268 | p.E14Q | 1 |
chr7:102114116-102114116 | p.K112E | 1 |
chr7:102114127-102114127 | p.A108V | 1 |
chr7:102114856-102114856 | p.A90A | 1 |
chr7:102114972-102114972 | p.K52E | 1 |
chr7:102116678-102116678 | p.C31C | 1 |
chr7:102116688-102116688 | p.P28H | 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 |   | 2 |   |   |   |   |   |   |   | 1 |   | 1 |   |   |   |   | 1 | 1 |   | 1 |
# mutation |   | 2 |   |   |   |   |   |   |   | 1 |   | 1 |   |   |   |   | 1 | 1 |   | 1 |
nonsynonymous SNV |   | 1 |   |   |   |   |   |   |   | 1 |   | 1 |   |   |   |   | 1 |   |   | 1 |
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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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 |
chr7:102119282 | p.A108V | 1 |
chr7:102114127 | p.A90A | 1 |
chr7:102114856 | p.K52E | 1 |
chr7:102114972 | p.C31C | 1 |
chr7:102116678 | p.P28H | 1 |
chr7:102116688 | p.E14Q | 1 |
chr7:102119268 | p.S9W | 1 |
Other DBs for Point Mutations |
Copy Number for POLR2J 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 POLR2J |
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 |
PPP1R35,CDK3,CENPT,FAM156A,FRZB,KMT2E-AS1,MOGS, MTCH1,NSUN5P1,NSUN5P2,PLOD3,POLR2J2,POLR2J3,POLR2J4, PRKRIP1,PRSS54,S100A1,TMUB1,TSC22D4,TTYH1,UPK3BL | ALS2CL,AQP5,AQP6,BTN2A1,CLK3,CRTC2,FAM131C, FLJ26850,GGA3,H3F3C,KCNK5,PI4KAP2,POLR2J2,POLR2J3, POLR2J4,POU5F1,PSORS1C2,QRICH2,TMEM80,VSIG10L,ZFYVE28 |
AHSA2,CRYGS,DMTF1,LINC01000,GIGYF1,HSF4,KRTAP5-1, LOC349114,LINC00174,NSUN5P1,PILRB,POLR2J3,POLR2J4,PRKRIP1, RRN3P1,SPDYE1,SPDYE5,SPDYE6,TTLL3,UPK3BL,WASH7P | AP4M1,MROH8,RTFDC1,CACNA2D3,FAM166B,ENDOV,FXYD7, GHSR,LOC100240735,LOC257358,MOAP1,NEK11,NPY,PLK5, POLR2J3,POLR2J4,POLR3GL,SPAG17,SPESP1,TRIM61,ZC4H2 |
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 POLR2J |
There's no related Drug. |
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Cross referenced IDs for POLR2J |
* 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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