Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for POLR1A
Basic gene info.Gene symbolPOLR1A
Gene namepolymerase (RNA) I polypeptide A, 194kDa
SynonymsA190|RPA1|RPA194|RPO1-4|RPO14
CytomapUCSC genome browser: 2p11.2
Genomic locationchr2 :86253450-86333278
Type of geneprotein-coding
RefGenesNM_015425.3,
Ensembl idENSG00000068654
DescriptionDNA-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 date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000068654
HPRD : 10161
Vega : OTTHUMG00000153165
ProteinUniProt: O95602
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR1A
BioGPS: 25885
Gene Expression Atlas: ENSG00000068654
The Human Protein Atlas: ENSG00000068654
PathwayNCI Pathway Interaction Database: POLR1A
KEGG: POLR1A
REACTOME: POLR1A
ConsensusPathDB
Pathway Commons: POLR1A
MetabolismMetaCyc: POLR1A
HUMANCyc: POLR1A
RegulationEnsembl's Regulation: ENSG00000068654
miRBase: chr2 :86,253,450-86,333,278
TargetScan: NM_015425
cisRED: ENSG00000068654
ContextiHOP: POLR1A
cancer metabolism search in PubMed: POLR1A
UCL Cancer Institute: POLR1A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for POLR1A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR1A
Familial Cancer Database: POLR1A
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM
KEGG_PYRIMIDINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: POLR1A
MedGen: POLR1A (Human Medical Genetics with Condition)
ClinVar: POLR1A
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPOLR1Achr28628723186287251chr28511094285110962
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows POLR1A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI742345METTL1711341142146479121465194POLR1A33448528625396686254117
BE550643POLR1A112628626898986269114PILRA12234279997379299974012

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=103)
Stat. for Synonymous SNVs
(# total SNVs=37)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr2:86259443-86259443p.G1408G5
chr2:86271264-86271264p.E1045K3
chr2:86269132-86269132p.R1151H2
chr2:86327173-86327173p.C67F2
chr2:86292415-86292415p.P680P2
chr2:86327194-86327194p.S60F2
chr2:86255054-86255054p.M1672I2
chr2:86276363-86276363p.V799M2
chr2:86274364-86274364p.H886L2
chr2:86270302-86270302p.Q1051P2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample783142 7161 1265  1318117
# mutation893162 7161 1675  1519122
nonsynonymous SNV552122 4141 1132  1113115
synonymous SNV3414  3 2  543  46 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr2:86254602p.G1703R2
chr2:86269132p.R1151H2
chr2:86327173p.C67F2
chr2:86327194p.S60F2
chr2:86266580p.R1249L2
chr2:86292455p.E942K1
chr2:86315739p.T779T1
chr2:86258525p.D501D1
chr2:86270118p.W1524L1
chr2:86302261p.P305P1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

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
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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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

: Open all cross reference information



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