Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 POLR1E
Basic gene info.Gene symbolPOLR1E
Gene namepolymerase (RNA) I polypeptide E, 53kDa
SynonymsPAF53|PRAF1
CytomapUCSC genome browser: 9p13.2
Genomic locationchr9 :37485944-37503693
Type of geneprotein-coding
RefGenesNM_001282766.1,
NM_022490.2,
Ensembl idENSG00000137054
DescriptionDNA-directed RNA polymerase I subunit EDNA-directed RNA polymerase I subunit RPA49RNA polymerase I subunit A49RNA polymerase I-associated factor 53polymerase (RNA) I associated factor 1
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000137054
HPRD : 15096
Vega : OTTHUMG00000019920
ProteinUniProt: Q9GZS1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR1E
BioGPS: 64425
Gene Expression Atlas: ENSG00000137054
The Human Protein Atlas: ENSG00000137054
PathwayNCI Pathway Interaction Database: POLR1E
KEGG: POLR1E
REACTOME: POLR1E
ConsensusPathDB
Pathway Commons: POLR1E
MetabolismMetaCyc: POLR1E
HUMANCyc: POLR1E
RegulationEnsembl's Regulation: ENSG00000137054
miRBase: chr9 :37,485,944-37,503,693
TargetScan: NM_001282766
cisRED: ENSG00000137054
ContextiHOP: POLR1E
cancer metabolism search in PubMed: POLR1E
UCL Cancer Institute: POLR1E
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for POLR1E(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR1E
Familial Cancer Database: POLR1E
* 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: POLR1E
MedGen: POLR1E (Human Medical Genetics with Condition)
ClinVar: POLR1E
PhenotypeMGI: POLR1E (International Mouse Phenotyping Consortium)
PhenomicDB: POLR1E

Mutations for POLR1E
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows POLR1E related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample        1        
GAIN (# sample)                 
LOSS (# sample)        1        
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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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=20)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr9:37492679-37492679p.A123A4
chr9:37495212-37495212p.L198L2
chr9:37501836-37501836p.E365D1
chr9:37486692-37486692p.?1
chr9:37493650-37493650p.R166H1
chr9:37495962-37495962p.L244R1
chr9:37503045-37503045p.M369T1
chr9:37486748-37486748p.T42I1
chr9:37493678-37493678p.I175I1
chr9:37498102-37498102p.V256A1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  7  2 3   1   14 5
# mutation1  5  2 3   1   14 5
nonsynonymous SNV1  3  1 1   1    3 4
synonymous SNV   2  1 2       11 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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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
chr9:37501715p.R325Q,POLR1E2
chr9:37501827p.K362K,POLR1E2
chr9:37487880p.T95T1
chr9:37498107p.R166H,POLR1E1
chr9:37487905p.I175I,POLR1E1
chr9:37500907p.A188V,POLR1E1
chr9:37489339p.P201S,POLR1E1
chr9:37493650p.E217K,POLR1E1
chr9:37493678p.N237N,POLR1E1
chr9:37501836p.S240L,POLR1E1

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 POLR1E 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 POLR1E

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

CDKN2A,IFRD1,KIAA0020,MYC,NPM3,PDSS1,POLR1E,
RCL1,RPS6,RPS7,SERBP1,SF3B14,STOML2,TEX10,
TOMM5,UCK2,UQCRH,UQCRHL,YBX1,ZBTB5,ZNF695
ACTR3B,CCNB1IP1,CHKA,CHRM1,DTNB,EIF3D,EIF3L,
GNB2L1,IMPDH2,KIAA0020,NACA,EPB41L4A-AS1,NOB1,NONO,
NPM1,POLR1E,RPL4,RPL5,RPS18,RPS6,RSL1D1

APTX,CLTA,DDX31,EEF1G,EXOSC3,FANCG,GNB2L1,
GRHPR,KIAA0020,NOB1,NOL6,POLR1E,RCL1,TRMT10B,
RPL7A,RPS6,SIGMAR1,SMU1,STOML2,TOMM5,ZCCHC7
ABHD14A,C2orf44,CUEDC2,DDX50,EEF1D,EIF3G,ELP2,
FBXO44,IRAK1BP1,LOC158572,LZTFL1,NAP1L1,POLR1E,RBMX2,
RPL12,RPL4,TCTN1,TMEM123,ZC3HC1,ZNF496,ZZZ3
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 POLR1E


There's no related Drug.
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Cross referenced IDs for POLR1E
* 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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