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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for POLR1A |
Basic gene info. | Gene symbol | POLR1A |
Gene name | polymerase (RNA) I polypeptide A, 194kDa | |
Synonyms | A190|RPA1|RPA194|RPO1-4|RPO14 | |
Cytomap | UCSC genome browser: 2p11.2 | |
Genomic location | chr2 :86253450-86333278 | |
Type of gene | protein-coding | |
RefGenes | NM_015425.3, | |
Ensembl id | ENSG00000068654 | |
Description | DNA-directed RNA polymerase I largest subunitDNA-directed RNA polymerase I subunit ADNA-directed RNA polymerase I subunit A1DNA-directed RNA polymerase I subunit RPA1RNA polymerase I 194 kDa subunitRNA polymerase I subunit A1 | |
Modification date | 20141207 | |
dbXrefs | HGNC : HGNC | |
Ensembl : ENSG00000068654 | ||
HPRD : 10161 | ||
Vega : OTTHUMG00000153165 | ||
Protein | UniProt: O95602 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_POLR1A | |
BioGPS: 25885 | ||
Gene Expression Atlas: ENSG00000068654 | ||
The Human Protein Atlas: ENSG00000068654 | ||
Pathway | NCI Pathway Interaction Database: POLR1A | |
KEGG: POLR1A | ||
REACTOME: POLR1A | ||
ConsensusPathDB | ||
Pathway Commons: POLR1A | ||
Metabolism | MetaCyc: POLR1A | |
HUMANCyc: POLR1A | ||
Regulation | Ensembl's Regulation: ENSG00000068654 | |
miRBase: chr2 :86,253,450-86,333,278 | ||
TargetScan: NM_015425 | ||
cisRED: ENSG00000068654 | ||
Context | iHOP: POLR1A | |
cancer metabolism search in PubMed: POLR1A | ||
UCL Cancer Institute: POLR1A | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for POLR1A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: POLR1A |
Familial Cancer Database: POLR1A |
* 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 |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: POLR1A |
MedGen: POLR1A (Human Medical Genetics with Condition) | |
ClinVar: POLR1A | |
Phenotype | MGI: POLR1A (International Mouse Phenotyping Consortium) |
PhenomicDB: POLR1A |
Mutations for POLR1A |
* 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 |
There's no inter-chromosomal structural variation. |
- 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 | POLR1A | chr2 | 86287231 | 86287251 | chr2 | 85110942 | 85110962 |
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 POLR1A 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 |
AI742345 | METTL17 | 11 | 341 | 14 | 21464791 | 21465194 | POLR1A | 334 | 485 | 2 | 86253966 | 86254117 | |
BE550643 | POLR1A | 1 | 126 | 2 | 86268989 | 86269114 | PILRA | 122 | 342 | 7 | 99973792 | 99974012 |
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=103) | (# total SNVs=37) |
(# total SNVs=2) | (# 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 |
chr2:86259443-86259443 | p.G1408G | 5 |
chr2:86271264-86271264 | p.E1045K | 3 |
chr2:86269132-86269132 | p.R1151H | 2 |
chr2:86327173-86327173 | p.C67F | 2 |
chr2:86292415-86292415 | p.P680P | 2 |
chr2:86327194-86327194 | p.S60F | 2 |
chr2:86255054-86255054 | p.M1672I | 2 |
chr2:86276363-86276363 | p.V799M | 2 |
chr2:86274364-86274364 | p.H886L | 2 |
chr2:86270302-86270302 | p.Q1051P | 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 | 7 | 8 | 3 | 14 | 2 |   | 7 | 1 | 6 | 1 |   | 12 | 6 | 5 |   |   | 13 | 18 | 1 | 17 |
# mutation | 8 | 9 | 3 | 16 | 2 |   | 7 | 1 | 6 | 1 |   | 16 | 7 | 5 |   |   | 15 | 19 | 1 | 22 |
nonsynonymous SNV | 5 | 5 | 2 | 12 | 2 |   | 4 | 1 | 4 | 1 |   | 11 | 3 | 2 |   |   | 11 | 13 | 1 | 15 |
synonymous SNV | 3 | 4 | 1 | 4 |   |   | 3 |   | 2 |   |   | 5 | 4 | 3 |   |   | 4 | 6 |   | 7 |
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 |
chr2:86269132 | p.C67F | 2 |
chr2:86327173 | p.S60F | 2 |
chr2:86327194 | p.R1249L | 2 |
chr2:86266580 | p.G1703R | 2 |
chr2:86254602 | p.R1151H | 2 |
chr2:86302279 | p.P927L | 1 |
chr2:86254644 | p.L681L | 1 |
chr2:86325778 | p.S1677S | 1 |
chr2:86259429 | p.P488L | 1 |
chr2:86272844 | p.D1513G | 1 |
Other DBs for Point Mutations |
Copy Number for POLR1A 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 POLR1A |
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 |
ANAPC1,ASXL2,COA7,CAD,DDX21,DOCK7,HUWE1, LOC284441,NUP155,NUP205,POLR1A,POLR1B,RAD54L2,RIF1, STRN,TET3,TRRAP,UBR4,USP34,WDR43,ZC3HAV1L | ANKRD52,ARID1A,ARL10,PRRC2B,NOP9,SOGA1,DFFA, GCN1L1,HERC2,HUWE1,INCENP,LMTK2,MDN1,KMT2B___KMT2D, NSD1,POLR1A,PRKDC,SMC1A,SRCAP,TRRAP,URB1 |
ANAPC1,CAD,CEP250,CHD7,FASN,MDN1,NEU3, PDCD11,PHF20,POLR1A,POLR1B,RIF1,SMPD4,SNRNP200, TCF20,TGFBRAP1,TTLL4,UHRF1BP1,USP36,XPO5,ZNF142 | ACACA,BMS1,NOP9,CAD,CKAP5,GCN1L1,HEATR1, ILF3,EMC1,LARP1,MDN1,NAT10,NUP188,NUP214, PDCD11,PFAS,POLR1A,PRKDC,URB1,XPO5,ZC3H18 |
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 POLR1A |
There's no related Drug. |
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Cross referenced IDs for POLR1A |
* 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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