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 POLR1D
Basic gene info.Gene symbolPOLR1D
Gene namepolymerase (RNA) I polypeptide D, 16kDa
SynonymsAC19|POLR1C|RPA16|RPA9|RPAC2|RPC16|RPO1-3|TCS2
CytomapUCSC genome browser: 13q12.2
Genomic locationchr13 :28194879-28241559
Type of geneprotein-coding
RefGenesNM_001206559.1,
NM_015972.3,NM_152705.2,
Ensembl idENSG00000186184
DescriptionDNA-directed RNA polymerase I subunit DDNA-directed RNA polymerases I and III subunit RPAC2RNA polymerases I and III subunit AC2
Modification date20141219
dbXrefs MIM : 613715
HGNC : HGNC
Ensembl : ENSG00000186184
HPRD : 14717
HPRD : 17877
Vega : OTTHUMG00000016635
ProteinUniProt: Q9Y2S0
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_POLR1D
BioGPS: 51082
Gene Expression Atlas: ENSG00000186184
The Human Protein Atlas: ENSG00000186184
PathwayNCI Pathway Interaction Database: POLR1D
KEGG: POLR1D
REACTOME: POLR1D
ConsensusPathDB
Pathway Commons: POLR1D
MetabolismMetaCyc: POLR1D
HUMANCyc: POLR1D
RegulationEnsembl's Regulation: ENSG00000186184
miRBase: chr13 :28,194,879-28,241,559
TargetScan: NM_001206559
cisRED: ENSG00000186184
ContextiHOP: POLR1D
cancer metabolism search in PubMed: POLR1D
UCL Cancer Institute: POLR1D
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for POLR1D(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: POLR1D
Familial Cancer Database: POLR1D
* 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 613715; gene.
613717; phenotype.
Orphanet 861; Treacher-Collins syndrome.
DiseaseKEGG Disease: POLR1D
MedGen: POLR1D (Human Medical Genetics with Condition)
ClinVar: POLR1D
PhenotypeMGI: POLR1D (International Mouse Phenotyping Consortium)
PhenomicDB: POLR1D

Mutations for POLR1D
* 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 POLR1D related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM544526POLR1D1769132824008228240850CHORDC1769993118994438389947307

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  2      1   
GAIN (# sample)      2      1   
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=10)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr13:28239940-28239940p.A73A4
chr13:28239925-28239925p.G68G2
chr13:28239970-28239970p.P83P2
chr13:28240029-28240029p.Y103C1
chr13:28240041-28240041p.R107Q1
chr13:28239952-28239952p.A77A1
chr13:28240074-28240074p.R118L1
chr13:28239962-28239962p.E81K1
chr13:28222568-28222568p.E27Q1
chr13:28239829-28239829p.K36K1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample33 6       21    2 5
# mutation33 7       21    2 5
nonsynonymous SNV23 7       21    1 3
synonymous SNV1                1 2
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
chr13:28239925p.G40G,POLR1D2
chr13:28197152p.R56P2
chr13:28197305p.P10S,POLR1D1
chr13:28240029p.N25H,POLR1D1
chr13:28222568p.E53K,POLR1D1
chr13:28240041p.H58L,POLR1D1
chr13:28239829p.R68R,POLR1D1
chr13:28240074p.G34E1
chr13:28239833p.A73T,POLR1D1
chr13:28197086p.S54F1

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 POLR1D 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 POLR1D

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

ALG5,EBPL,EXOSC8,GTF2F2,GTF3A,HMGB1,LNX2,
MRPL57,MTIF3,N6AMT2,PAN3,POLR1D,POMP,RNASEH2B,
RPL21,RPL24,RPL38,RPS13,RPS29,SAP18,TPT1
C18orf21,EIF3H,EIF3M,HINT1,IGBP1,LINC00493,LRRC75A-AS1,
PCBP2,POLR1D,RPL22,RPL30,RPL32,RPL35A,RPL38,
RPL41,RPL6,RPS13,RPS15A,RPS23,RPS29,TIMM9

ALG5,CDK8,COMMD6,MICU2,GTF2F2,GTF3A,GPALPP1,
LNX2,MED4,MRPL57,MRPS31,MTIF3,NUFIP1,PAN3,
PCID2,POLR1D,POMP,RNASEH2B,RNF6,SAP18,UBAC2
BOLA1,C12orf10,APOPT1,DGCR6L,EEF1A1,ELP2,FAM175A,
KBTBD3,KLHDC3,MRPL10,NACA,POLR1D,PPIE,R3HCC1,
RBMX2,RPL15,THAP11,THYN1,VPS72,ZDHHC4,ZMAT5
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 POLR1D


There's no related Drug.
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Cross referenced IDs for POLR1D
* 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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