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 POLR2L
Basic gene info.Gene symbolPOLR2L
Gene namepolymerase (RNA) II (DNA directed) polypeptide L, 7.6kDa
SynonymsRBP10|RPABC5|RPB10|RPB10beta|RPB7.6|hRPB7.6
CytomapUCSC genome browser: 11p15
Genomic locationchr11 :839720-842529
Type of geneprotein-coding
RefGenesNM_021128.4,
Ensembl idENSG00000177700
DescriptionDNA-directed RNA polymerase III subunit LDNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase II 7.6 kDa subunitRNA polymerases I, II, and III subunit ABC5RPB10 homolog
Modification date20141207
dbXrefs MIM : 601189
HGNC : HGNC
Ensembl : ENSG00000177700
HPRD : 01155
Vega : OTTHUMG00000133316
ProteinUniProt: P62875
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR2L
BioGPS: 5441
Gene Expression Atlas: ENSG00000177700
The Human Protein Atlas: ENSG00000177700
PathwayNCI Pathway Interaction Database: POLR2L
KEGG: POLR2L
REACTOME: POLR2L
ConsensusPathDB
Pathway Commons: POLR2L
MetabolismMetaCyc: POLR2L
HUMANCyc: POLR2L
RegulationEnsembl's Regulation: ENSG00000177700
miRBase: chr11 :839,720-842,529
TargetScan: NM_021128
cisRED: ENSG00000177700
ContextiHOP: POLR2L
cancer metabolism search in PubMed: POLR2L
UCL Cancer Institute: POLR2L
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for POLR2L(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR2L
Familial Cancer Database: POLR2L
* 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 601189; gene.
Orphanet
DiseaseKEGG Disease: POLR2L
MedGen: POLR2L (Human Medical Genetics with Condition)
ClinVar: POLR2L
PhenotypeMGI: POLR2L (International Mouse Phenotyping Consortium)
PhenomicDB: POLR2L

Mutations for POLR2L
* 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 POLR2L 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
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=3)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr11:840477-840477p.D33D3
chr11:842499-842499p.P4S3
chr11:840428-840428p.L50L1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample      1  1      1   
# mutation      1  1      1   
nonsynonymous SNV      1         1   
synonymous SNV         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
chr11:840420p.L50L1
chr11:840428p.A37D1
chr11:840466p.H52Q1

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 POLR2L 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 POLR2L

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

ALKBH7,ARL6IP4,TSR3,C19orf24,LAMTOR4,CHCHD5,EDF1,
FAM173A,FBXL15,FIS1,MRPL23,MRPL53,MRPL54,NME3,
NUDT22,PHPT1,POLR2L,STUB1,TMEM160,TSSC4,UQCR11
AP1M1,ARL2,BCAP31,BLOC1S1,CCDC107,CD63,GPX1,
GPX4,HINT2,LGALS1,LRP3,MRPS11,MYL6,NDUFAF3,
PHLDA3,POLR2E,POLR2L,PSMD8,RNPEPL1,TST,UROD

ATP5D,AURKAIP1,UQCC3,CENPM,COPE,EIF5A,EIF5AL1,
GADD45GIP1,HMBS,NAA38,MRPL20,MRPL54,MRPS34,NDUFS3,
POLR2L,PSMD9,RPS6KB2,SERF2,SIVA1,SSSCA1,STRA13
TMEM258,HYPK,CCDC167,GADD45GIP1,MRPL20,MRPL51,MRPL52,
MYEOV2,NDUFA7,NEDD8,PFDN6,POLR2L,PSMA7,PSMB1,
PSMB4,PSMB6,PSMB7,PSMD13,PSMD8,RBX1,SNRPC
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 POLR2L


There's no related Drug.
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Cross referenced IDs for POLR2L
* 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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