Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 POLR1C
Basic gene info.Gene symbolPOLR1C
Gene namepolymerase (RNA) I polypeptide C, 30kDa
SynonymsRPA39|RPA40|RPA5|RPAC1|TCS3
CytomapUCSC genome browser: 6p21.1
Genomic locationchr6 :43484776-43489246
Type of geneprotein-coding
RefGenesNM_203290.2,
NM_004875.2,
Ensembl idENSG00000171453
DescriptionAC40DNA-directed RNA polymerase I subunit CDNA-directed RNA polymerases I and III 40 kDa polypeptideDNA-directed RNA polymerases I and III subunit RPAC1RNA polymerases I and III subunit AC1RPC40
Modification date20141219
dbXrefs MIM : 610060
HGNC : HGNC
Ensembl : ENSG00000171453
HPRD : 09661
Vega : OTTHUMG00000014739
ProteinUniProt: O15160
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR1C
BioGPS: 9533
Gene Expression Atlas: ENSG00000171453
The Human Protein Atlas: ENSG00000171453
PathwayNCI Pathway Interaction Database: POLR1C
KEGG: POLR1C
REACTOME: POLR1C
ConsensusPathDB
Pathway Commons: POLR1C
MetabolismMetaCyc: POLR1C
HUMANCyc: POLR1C
RegulationEnsembl's Regulation: ENSG00000171453
miRBase: chr6 :43,484,776-43,489,246
TargetScan: NM_203290
cisRED: ENSG00000171453
ContextiHOP: POLR1C
cancer metabolism search in PubMed: POLR1C
UCL Cancer Institute: POLR1C
Assigned class in ccmGDBB - This gene belongs to cancer gene.

Top
Phenotypic Information for POLR1C(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR1C
Familial Cancer Database: POLR1C
* 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 248390; phenotype.
610060; gene.
Orphanet 861; Treacher-Collins syndrome.
DiseaseKEGG Disease: POLR1C
MedGen: POLR1C (Human Medical Genetics with Condition)
ClinVar: POLR1C
PhenotypeMGI: POLR1C (International Mouse Phenotyping Consortium)
PhenomicDB: POLR1C

Mutations for POLR1C
* 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 POLR1C 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

Top
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)

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=19)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr6:43488089-43488089p.V193V4
chr6:43488045-43488045p.G179W2
chr6:43488991-43488991p.K332Q2
chr6:43489029-43489029p.Q344Q2
chr6:43487460-43487460p.V89G2
chr6:43487902-43487902p.E161K1
chr6:43488439-43488439p.P244P1
chr6:43484870-43484870p.E8V1
chr6:43487911-43487911p.V164M1
chr6:43488442-43488442p.V245V1

Top
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
# sample11 2  1 4  111  22 2
# mutation11 4  1 3  111  22 2
nonsynonymous SNV11 4  1 2   11  11 2
synonymous SNV        1  1    11  
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])

Top
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
chr6:43488991p.K332Q3
chr6:43488442p.C214R1
chr6:43484915p.A229T1
chr6:43488447p.A231T1
chr6:43485064p.V245M1
chr6:43488713p.V245V1
chr6:43487162p.G247V1
chr6:43488739p.F283F1
chr6:43487172p.K292M1
chr6:43487902p.A2V1

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 POLR1C 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]

Top
Gene Expression for POLR1C

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

: Open all plots for all cancer types


Top
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

AARS2,ABCC10,DNPH1,RRP36,GTPBP2,HSP90AB1,KLHDC3,
MAD2L1BP,MEA1,MRPL14,MRPL2,MRPS10,MRPS18A,POLR1C,
PPP2R5D,SLC35B2,SNRPC,TBCC,TJAP1,TOMM6,XPO5
ALKBH2,DKC1,DTNB,EIF3D,ELMO3,FBL,H2AFY2,
IMPDH2,KRTCAP3,LAD1,MRTO4,NPM3,POLR1C,PPAP2C,
PRSS8,RAB25,RPL3,RTKN,TOMM34,TP53,TRIM27

ABT1,BYSL,CCDC58,ECE2,GADD45GIP1,LSM2,MAD2L1BP,
MEA1,MRPL11,MRPL14,MRPL2,POLR1C,PPIL1,RPS10,
RPS18,SRSF3,SRSF7,SNRPC,TBCC,TOMM6,ZNRD1
BNIP1,BOLA3,CCT2,DCAF13,ENOPH1,GNL3,MRPL3,
MRTO4,NHP2,NHP2L1,NME2,NR2C2AP,NUP37,PAK1IP1,
PDCD2,POLR1C,POLR2D,PTRH2,SNRNP40,SRPRB,TOMM6
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for POLR1C


There's no related Drug.
Top
Cross referenced IDs for POLR1C
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas