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 POLR2E

Basic gene info.	Gene symbol	POLR2E
	Gene name	polymerase (RNA) II (DNA directed) polypeptide E, 25kDa
	Synonyms	RPABC1\|RPB5\|XAP4\|hRPB25\|hsRPB5
	Cytomap	UCSC genome browser: 19p13.3
	Genomic location	chr19 :1086577-1095391
	Type of gene	protein-coding
	RefGenes	NM_002695.3,
	Ensembl id	ENSG00000099817
	Description	DNA directed RNA polymerase II 23 kda polypeptideDNA-directed RNA polymerase II 23 kDa polypeptideDNA-directed RNA polymerase II subunit EDNA-directed RNA polymerase subunit RPABC1DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymera
	Modification date	20141207
dbXrefs	MIM : 180664
	HGNC : HGNC
	Ensembl : ENSG00000099817
	HPRD : 15946
	Vega : OTTHUMG00000181873
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_POLR2E
	BioGPS: 5434
	Gene Expression Atlas: ENSG00000099817
	The Human Protein Atlas: ENSG00000099817
Pathway	NCI Pathway Interaction Database: POLR2E
	KEGG: POLR2E
	REACTOME: POLR2E
	ConsensusPathDB
	Pathway Commons: POLR2E
Metabolism	MetaCyc: POLR2E
	HUMANCyc: POLR2E
Regulation	Ensembl's Regulation: ENSG00000099817
	miRBase: chr19 :1,086,577-1,095,391
	TargetScan: NM_002695
	cisRED: ENSG00000099817
Context	iHOP: POLR2E
	cancer metabolism search in PubMed: POLR2E
	UCL Cancer Institute: POLR2E
Assigned class in ccmGDB	C

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Phenotypic Information for POLR2E(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: POLR2E
	Familial Cancer Database: POLR2E

* 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: POLR2E
	MedGen: POLR2E (Human Medical Genetics with Condition)
	ClinVar: POLR2E
Phenotype	MGI: POLR2E (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: POLR2E

Mutations for POLR2E

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows POLR2E 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
BQ362075	POLR2E	26	376	19	1093473	1093828	POLR2E	366	424	19	1093934	1093992
CB215068	POLR2E	12	84	19	1091856	1093926	POLR2E	82	570	19	1088615	1091875
BF898728	CD82	37	267	11	44628137	44628366	POLR2E	264	337	19	1094579	1094652

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=1

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=14)	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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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
chr19:1090905-1090905	p.?	2
chr19:1091841-1091841	p.T100S	1
chr19:1094056-1094056	p.L27V	1
chr19:1090119-1090119	p.T152I	1
chr19:1091854-1091854	p.Q95Q	1
chr19:1094062-1094062	p.G25S	1
chr19:1091857-1091857	p.M94I	1
chr19:1095267-1095267	p.T16T	1
chr19:1090909-1090909	p.E143K	1
chr19:1091891-1091891	p.G83D	1

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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=1

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	1			2					1			3	2				3	3	1	4
# mutation	1			2					1			3	2				3	3	1	4
nonsynonymous SNV	1			2					1			2	1				1	1		2
synonymous SNV												1	1				2	2	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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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
chr19:1094045	p.T111T	1
chr19:1090971	p.I104I	1
chr19:1094056	p.T100S	1
chr19:1090978	p.Q95Q	1
chr19:1094062	p.E79E	1
chr19:1091806	p.D57N	1
chr19:1095300	p.R52R	1
chr19:1091827	p.S44S	1
chr19:1095303	p.R172M	1
chr19:1091841	p.Q30Q	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 POLR2E 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 POLR2E

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


ATP5D,C19orf24,TMEM259,ABHD17A,GPX4,MAP2K2,MBD3, MED16,NCLN,NDUFS7,OAZ1,PLEKHJ1,POLR2E,POLRMT, RNF126,SGTA,SIRT6,STK11,TIMM13,UQCR11,WDR18	AGPAT2,AP1M1,ASCC2,ADIRF,CNPPD1,CAMK1,ETFB, FPGS,FURIN,GPX4,GYPC,LRP3,PHLDA3,POLR2E, PRR5,RXRA,SCRN2,SLC2A4RG,TALDO1,TESK1,TST

ATP5D,UQCC3,C19orf24,CCDC124,CLPP,FARSA,LSM4, MRPL4,NCLN,NDUFS7,POLR2E,RNF126,RUVBL2,SGTA, SNRPA,ALYREF,THOP1,TIMM13,TMEM161A,TOMM40,WDR18	ACD,AP2M1,ARL2,CCDC124,COPS6,DEXI,EEF1D, EMD,JMJD8,PIN1,POLR2E,PRPF31,RAD23A,RNASEH2C, RNH1,RPP21,SGTA,SIRT2,SLC2A8,THAP7,TSSC4

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 POLR2E

There's no related Drug.

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Cross referenced IDs for POLR2E

* 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