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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for POLR2D |
Basic gene info. | Gene symbol | POLR2D |
Gene name | polymerase (RNA) II (DNA directed) polypeptide D | |
Synonyms | HSRBP4|HSRPB4|RBP4|RPB16 | |
Cytomap | UCSC genome browser: 2q21 | |
Genomic location | chr2 :128603839-128615729 | |
Type of gene | protein-coding | |
RefGenes | NM_004805.3, | |
Ensembl id | ENSG00000144231 | |
Description | DNA-directed RNA polymerase II 16 kDa polypeptideDNA-directed RNA polymerase II subunit DDNA-directed RNA polymerase II subunit RPB4RNA polymerase II 16 kDa subunitRNA polymerase II subunit B4RNA polymerase II subunit hsRBP4 | |
Modification date | 20141207 | |
dbXrefs | MIM : 606017 | |
HGNC : HGNC | ||
Ensembl : ENSG00000144231 | ||
HPRD : 16191 | ||
Vega : OTTHUMG00000131531 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_POLR2D | |
BioGPS: 5433 | ||
Gene Expression Atlas: ENSG00000144231 | ||
The Human Protein Atlas: ENSG00000144231 | ||
Pathway | NCI Pathway Interaction Database: POLR2D | |
KEGG: POLR2D | ||
REACTOME: POLR2D | ||
ConsensusPathDB | ||
Pathway Commons: POLR2D | ||
Metabolism | MetaCyc: POLR2D | |
HUMANCyc: POLR2D | ||
Regulation | Ensembl's Regulation: ENSG00000144231 | |
miRBase: chr2 :128,603,839-128,615,729 | ||
TargetScan: NM_004805 | ||
cisRED: ENSG00000144231 | ||
Context | iHOP: POLR2D | |
cancer metabolism search in PubMed: POLR2D | ||
UCL Cancer Institute: POLR2D | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for POLR2D(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: POLR2D |
Familial Cancer Database: POLR2D |
* 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: POLR2D |
MedGen: POLR2D (Human Medical Genetics with Condition) | |
ClinVar: POLR2D | |
Phenotype | MGI: POLR2D (International Mouse Phenotyping Consortium) |
PhenomicDB: POLR2D |
Mutations for POLR2D |
* 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 POLR2D 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 |
BU183660 | PSMC3 | 1 | 420 | 11 | 47440326 | 47442202 | POLR2D | 421 | 487 | 2 | 128605647 | 128605713 |
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=13) | (# total SNVs=0) |
(# 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 |
chr2:128610580-128610580 | p.S58L | 2 |
chr2:128608249-128608249 | p.Q89* | 1 |
chr2:128610503-128610503 | p.R84C | 1 |
chr2:128610508-128610508 | p.S82N | 1 |
chr2:128610524-128610524 | p.R77* | 1 |
chr2:128610526-128610526 | p.N76S | 1 |
chr2:128605685-128605685 | p.Y142C | 1 |
chr2:128610535-128610535 | p.R73H | 1 |
chr2:128605740-128605740 | p.D124H | 1 |
chr2:128610554-128610554 | p.Y67H | 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 |   |   | 2 |   |   | 1 |   |   |   |   | 3 |   |   |   |   |   |   |   | 3 |
# mutation | 1 |   |   | 2 |   |   | 1 |   |   |   |   | 3 |   |   |   |   |   |   |   | 3 |
nonsynonymous SNV | 1 |   |   | 2 |   |   | 1 |   |   |   |   | 3 |   |   |   |   |   |   |   | 3 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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 |
chr2:128610526 | p.Y142C | 1 |
chr2:128610545 | p.D124G | 1 |
chr2:128610554 | p.E109K | 1 |
chr2:128610608 | p.K91R | 1 |
chr2:128605685 | p.R84C | 1 |
chr2:128605739 | p.S82N | 1 |
chr2:128608189 | p.N76S | 1 |
chr2:128608242 | p.R70S | 1 |
chr2:128610503 | p.Y67H | 1 |
chr2:128610508 | p.E49Q | 1 |
Other DBs for Point Mutations |
Copy Number for POLR2D 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 POLR2D |
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 |
AMMECR1L,BUB1,CCDC138,CCNB2,CENPA,CKAP2L,DDX18, ERCC3,GMPS,IWS1,MCM6,NIFK,MYBL2,NCAPH, POLR1B,POLR2D,SAP130,TPX2,TRIP13,TTL,WDR33 | FAM210A,CPEB3,CUL3,CUL5,EXOC6,FAM160A1,FASTKD1, FASTKD5,GFM2,HSF2,MED14,OTUD4,POLR2D,PTP4A1, SACS,TMEM65,UBE3A,USP28,USP38,XK,ZBTB43 |
BCS1L,BIRC5,CCT4,CCT7,CIAO1,CPSF3,DCUN1D5, DDX18,DTYMK,NIFK,MRPL30,PNO1,PNPT1,POLR2D, PSMD14,PTCD3,USP39,WDR12,WDR43,WDR75,ZC3H15 | ABCE1,BRIX1,CCDC138,CCT2,DNAJA3,GNL3,MRPL3, MRTO4,NOP16,PAK1IP1,PGAM5,PNO1,POLR1C,POLR2D, PTRH2,TRMT10C,RPP40,SRPRB,TIMM50,UBA2,UTP6 |
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 POLR2D |
There's no related Drug. |
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Cross referenced IDs for POLR2D |
* 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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