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 POLR2I
Basic gene info.Gene symbolPOLR2I
Gene namepolymerase (RNA) II (DNA directed) polypeptide I, 14.5kDa
SynonymsRPB9|hRPB14.5
CytomapUCSC genome browser: 19q12
Genomic locationchr19 :36604610-36606206
Type of geneprotein-coding
RefGenesNM_006233.4,
Ensembl idENSG00000105258
DescriptionDNA-directed RNA polymerase II 14.5 kDa polypeptideDNA-directed RNA polymerase II subunit IDNA-directed RNA polymerase II subunit RPB9RNA polymerase II 14.5 kDa subunitRNA polymerase II subunit B9RPB14.5
Modification date20141207
dbXrefs MIM : 180662
HGNC : HGNC
Ensembl : ENSG00000105258
HPRD : 15944
Vega : OTTHUMG00000181749
ProteinUniProt: P36954
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR2I
BioGPS: 5438
Gene Expression Atlas: ENSG00000105258
The Human Protein Atlas: ENSG00000105258
PathwayNCI Pathway Interaction Database: POLR2I
KEGG: POLR2I
REACTOME: POLR2I
ConsensusPathDB
Pathway Commons: POLR2I
MetabolismMetaCyc: POLR2I
HUMANCyc: POLR2I
RegulationEnsembl's Regulation: ENSG00000105258
miRBase: chr19 :36,604,610-36,606,206
TargetScan: NM_006233
cisRED: ENSG00000105258
ContextiHOP: POLR2I
cancer metabolism search in PubMed: POLR2I
UCL Cancer Institute: POLR2I
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for POLR2I(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR2I
Familial Cancer Database: POLR2I
* 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 180662; gene.
Orphanet
DiseaseKEGG Disease: POLR2I
MedGen: POLR2I (Human Medical Genetics with Condition)
ClinVar: POLR2I
PhenotypeMGI: POLR2I (International Mouse Phenotyping Consortium)
PhenomicDB: POLR2I

Mutations for POLR2I
* 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 POLR2I related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA230064POLR2I1266193660585836606123LAMP2262547X119589342119603043
AA165636POLR2I3145193660461636604957DBI1425322120124574120129966

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=9)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr19:36605261-36605261p.N56K2
chr19:36605572-36605572p.L35V2
chr19:36605602-36605602p.Y25H2
chr19:36605736-36605736p.E8V1
chr19:36604965-36604965p.C89C1
chr19:36605737-36605737p.E8Q1
chr19:36605124-36605124p.S73F1
chr19:36605738-36605738p.Y7*1
chr19:36605140-36605140p.I68V1
chr19:36605757-36605757p.M1T1

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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
# sample11 1    1       2  1
# mutation11 1    1       2  1
nonsynonymous SNV1  1    1       1   
synonymous SNV 1              1  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
chr19:36605708p.E8V1
chr19:36605736p.E8Q1
chr19:36605737p.A116A1
chr19:36604687p.A102V1
chr19:36604927p.C89C1
chr19:36604965p.Q18H1
chr19:36605705p.C17C1

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 POLR2I 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 POLR2I

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

C19orf43,LAMTOR4,CAPNS1,CCDC12,COX6B1,ETV2,GADD45GIP1,
LIN37,LSM7,NDUFA11,NDUFA13,NDUFB11,NDUFB7,POLR2I,
RBM42,RFXANK,RPS16,SDHAF1,SNRPD2,TBCB,TMEM147
ALKBH7,RPP25L,CHCHD2,COX4I1,ECI1,DCTN3,ECSIT,
EIF3K,IDH3G,MRPL11,MRPL43,MRPL51,MRPS18A,NDUFA11,
NDUFA13,NDUFB7,NOSIP,POLR2I,TXN2,UBE2M,ZNF511

ANAPC11,CLPP,COX6B1,EXOSC5,GADD45GIP1,GEMIN7,LSM7,
MRPS12,NDUFA11,NDUFA13,POLR2I,PRMT1,RPL18,RPS16,
RUVBL2,SDHAF1,SNRPD2,TBCB,TIMM50,TMEM147,TRAPPC5
ANAPC11,ARL6IP4,BABAM1,FAU,FIS1,MRPL57,MRPL43,
MRPS24,LINC00116,NDUFA11,NDUFA13,NDUFB7,NUBP2,POLR2F,
POLR2I,PQBP1,PRDX2,RPP21,RPS16,THAP7,TIMM17B
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 POLR2I


There's no related Drug.
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Cross referenced IDs for POLR2I
* 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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