Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 POLR1A

Basic gene info.	Gene symbol	POLR1A
	Gene name	polymerase (RNA) I polypeptide A, 194kDa
	Synonyms	A190\|RPA1\|RPA194\|RPO1-4\|RPO14
	Cytomap	UCSC genome browser: 2p11.2
	Genomic location	chr2 :86253450-86333278
	Type of gene	protein-coding
	RefGenes	NM_015425.3,
	Ensembl id	ENSG00000068654
	Description	DNA-directed RNA polymerase I largest subunitDNA-directed RNA polymerase I subunit ADNA-directed RNA polymerase I subunit A1DNA-directed RNA polymerase I subunit RPA1RNA polymerase I 194 kDa subunitRNA polymerase I subunit A1
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000068654
	HPRD : 10161
	Vega : OTTHUMG00000153165
Protein	UniProt: O95602 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_POLR1A
	BioGPS: 25885
	Gene Expression Atlas: ENSG00000068654
	The Human Protein Atlas: ENSG00000068654
Pathway	NCI Pathway Interaction Database: POLR1A
	KEGG: POLR1A
	REACTOME: POLR1A
	ConsensusPathDB
	Pathway Commons: POLR1A
Metabolism	MetaCyc: POLR1A
	HUMANCyc: POLR1A
Regulation	Ensembl's Regulation: ENSG00000068654
	miRBase: chr2 :86,253,450-86,333,278
	TargetScan: NM_015425
	cisRED: ENSG00000068654
Context	iHOP: POLR1A
	cancer metabolism search in PubMed: POLR1A
	UCL Cancer Institute: POLR1A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for POLR1A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: POLR1A
	Familial Cancer Database: POLR1A

* 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/

Metabolic Pathway Description
KEGG_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: POLR1A
	MedGen: POLR1A (Human Medical Genetics with Condition)
	ClinVar: POLR1A
Phenotype	MGI: POLR1A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: POLR1A

Mutations for POLR1A

* 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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	POLR1A	chr2	86287231	86287251		chr2	85110942	85110962

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows POLR1A related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AI742345	METTL17	11	341	14	21464791	21465194	POLR1A	334	485	2	86253966	86254117
BE550643	POLR1A	1	126	2	86268989	86269114	PILRA	122	342	7	99973792	99974012

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=103)	Stat. for Synonymous SNVs (# total SNVs=37)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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Top 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 position	Mutation(aa)	Unique sampleID count
chr2:86259443-86259443	p.G1408G	5
chr2:86271264-86271264	p.E1045K	3
chr2:86269132-86269132	p.R1151H	2
chr2:86327173-86327173	p.C67F	2
chr2:86292415-86292415	p.P680P	2
chr2:86327194-86327194	p.S60F	2
chr2:86255054-86255054	p.M1672I	2
chr2:86276363-86276363	p.V799M	2
chr2:86274364-86274364	p.H886L	2
chr2:86270302-86270302	p.Q1051P	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	7	8	3	14	2		7	1	6	1		12	6	5			13	18	1	17
# mutation	8	9	3	16	2		7	1	6	1		16	7	5			15	19	1	22
nonsynonymous SNV	5	5	2	12	2		4	1	4	1		11	3	2			11	13	1	15
synonymous SNV	3	4	1	4			3		2			5	4	3			4	6		7

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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr2:86269132	p.C67F	2
chr2:86327173	p.S60F	2
chr2:86327194	p.R1249L	2
chr2:86266580	p.G1703R	2
chr2:86254602	p.R1151H	2
chr2:86302279	p.P927L	1
chr2:86254644	p.L681L	1
chr2:86325778	p.S1677S	1
chr2:86259429	p.P488L	1
chr2:86272844	p.D1513G	1

Other 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

Copy Number for POLR1A 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 POLR1A

Gene 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.

Differential 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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CNV 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

Co-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


ANAPC1,ASXL2,COA7,CAD,DDX21,DOCK7,HUWE1, LOC284441,NUP155,NUP205,POLR1A,POLR1B,RAD54L2,RIF1, STRN,TET3,TRRAP,UBR4,USP34,WDR43,ZC3HAV1L	ANKRD52,ARID1A,ARL10,PRRC2B,NOP9,SOGA1,DFFA, GCN1L1,HERC2,HUWE1,INCENP,LMTK2,MDN1,KMT2B___KMT2D, NSD1,POLR1A,PRKDC,SMC1A,SRCAP,TRRAP,URB1

ANAPC1,CAD,CEP250,CHD7,FASN,MDN1,NEU3, PDCD11,PHF20,POLR1A,POLR1B,RIF1,SMPD4,SNRNP200, TCF20,TGFBRAP1,TTLL4,UHRF1BP1,USP36,XPO5,ZNF142	ACACA,BMS1,NOP9,CAD,CKAP5,GCN1L1,HEATR1, ILF3,EMC1,LARP1,MDN1,NAT10,NUP188,NUP214, PDCD11,PFAS,POLR1A,PRKDC,URB1,XPO5,ZC3H18

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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 POLR1A

There's no related Drug.

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Cross referenced IDs for POLR1A

* 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