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 POLR2F
Basic gene info.Gene symbolPOLR2F
Gene namepolymerase (RNA) II (DNA directed) polypeptide F
SynonymsHRBP14.4|POLRF|RPABC14.4|RPABC2|RPB14.4|RPB6|RPC15
CytomapUCSC genome browser: 22q13.1
Genomic locationchr22 :38349673-38365319
Type of geneprotein-coding
RefGenesNM_001301129.1,
NM_001301130.1,NM_001301131.1,NM_021974.4,NR_125371.1,
Ensembl idENSG00000100142
DescriptionDNA-directed RNA polymerase II subunit FDNA-directed RNA polymerases I, II, and III 14.4 kDa polypeptideDNA-directed RNA polymerases I, II, and III subunit RPABC2RNA Polymerase II subunit 14.4 kDRNA polymerases I, II, and III subunit ABC2
Modification date20141207
dbXrefs MIM : 604414
HGNC : HGNC
Ensembl : ENSG00000100142
HPRD : 05105
Vega : OTTHUMG00000151160
ProteinUniProt: P61218
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR2F
BioGPS: 5435
Gene Expression Atlas: ENSG00000100142
The Human Protein Atlas: ENSG00000100142
PathwayNCI Pathway Interaction Database: POLR2F
KEGG: POLR2F
REACTOME: POLR2F
ConsensusPathDB
Pathway Commons: POLR2F
MetabolismMetaCyc: POLR2F
HUMANCyc: POLR2F
RegulationEnsembl's Regulation: ENSG00000100142
miRBase: chr22 :38,349,673-38,365,319
TargetScan: NM_001301129
cisRED: ENSG00000100142
ContextiHOP: POLR2F
cancer metabolism search in PubMed: POLR2F
UCL Cancer Institute: POLR2F
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of POLR2F in cancer cell metabolism1. Król M, Polańska J, Pawłowski K, Turowski P, Skierski J, et al. (2010) Transcriptomic signature of cell lines isolated from canine mammary adenocarcinoma metastases to lungs. Journal of applied genetics 51: 37-50. go to article

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Phenotypic Information for POLR2F(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR2F
Familial Cancer Database: POLR2F
* 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 604414; gene.
Orphanet
DiseaseKEGG Disease: POLR2F
MedGen: POLR2F (Human Medical Genetics with Condition)
ClinVar: POLR2F
PhenotypeMGI: POLR2F (International Mouse Phenotyping Consortium)
PhenomicDB: POLR2F

Mutations for POLR2F
* 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 POLR2F related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI367319POLR2F5400223836832238368717LRFN3396485193642830036428389
BF961261POLR2F25291223836856838368835PIH1D1276307194994991749949948

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)             1   
LOSS (# sample)                 
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr22:38355370-38355370p.V36V3
chr22:38352789-38352789p.G10G2
chr22:38355418-38355418p.I52M1
chr22:38363691-38363691p.W118*1
chr22:38349806-38349806p.N4K1
chr22:38355426-38355426p.P55L1
chr22:38355440-38355440p.Y60N1
chr22:38352790-38352790p.D11N1
chr22:38355453-38355453p.R64H1
chr22:38352792-38352792p.D11D1

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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
# sample22 1     1 1    33  
# mutation22 1     1 1    33  
nonsynonymous SNV12 1     1 1    11  
synonymous SNV1               22  
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
chr22:38355471p.N4K1
chr22:38349806p.D11N1
chr22:38355472p.D11D1
chr22:38352790p.E20K1
chr22:38363644p.V36V1
chr22:38352792p.I52M1
chr22:38352817p.P55L1
chr22:38355370p.V65M1
chr22:38355418p.R69R1
chr22:38355426p.R69Q1

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 POLR2F 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 POLR2F

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

ANKRD54,CCDC124,DGCR14,LOC152217,LSM7,MPST,NHP2L1,
NOL12,PES1,PFDN2,POLR2F,RANBP1,RPS19,RPS19BP1,
RRP1,RRP7A,SHFM1,SNRPA,TOMM22,TRMU,TSPO
DGCR6L,EDF1,EEF1D,EIF3G,FAU,MPG,MRPL28,
MRPS34,NT5C,NUDC,PFDN6,PIH1D1,PMVK,POLR2F,
PRDX5,PRPF31,R3HCC1,NELFE,SURF2,TMED1,ZNF622

ADSL,ATP5J2,BID,COX7B,DRG1,MRPL40,MRPS15,
MRPS23,MYEOV2,NHP2,NHP2L1,NME1,PHF5A,POLR2F,
PPIH,RANBP1,RBX1,SNRPG,TIMM8B,TOMM22,TXN2
ANAPC11,ARL6IP4,BUD31,C19orf53,FIS1,HAX1,MYEOV2,
LINC00116,NDUFA11,NDUFA7,NDUFB6,NDUFB8,OST4,POLR2F,
PRDX2,PSMD8,PSMD9,SCNM1,SIVA1,EMC4,TRAPPC3
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 POLR2F


There's no related Drug.
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Cross referenced IDs for POLR2F
* 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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