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 POLR2A

Basic gene info.	Gene symbol	POLR2A
	Gene name	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa
	Synonyms	POLR2\|POLRA\|RPB1\|RPBh1\|RPO2\|RPOL2\|RpIILS\|hRPB220\|hsRPB1
	Cytomap	UCSC genome browser: 17p13.1
	Genomic location	chr17 :7387697-7417935
	Type of gene	protein-coding
	RefGenes	NM_000937.4,
	Ensembl id	ENSG00000181222
	Description	DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunitDNA-directed RNA polymerase II subunit ADNA-directed RNA polymerase II subunit RPB1DNA-directed RNA polymerase III largest subunitRNA polymerase II subunit B1RNA-directed
	Modification date	20141207
dbXrefs	MIM : 180660
	HGNC : HGNC
	Ensembl : ENSG00000181222
	HPRD : 08916
	Vega : OTTHUMG00000177594
Protein	UniProt: P24928 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_POLR2A
	BioGPS: 5430
	Gene Expression Atlas: ENSG00000181222
	The Human Protein Atlas: ENSG00000181222
Pathway	NCI Pathway Interaction Database: POLR2A
	KEGG: POLR2A
	REACTOME: POLR2A
	ConsensusPathDB
	Pathway Commons: POLR2A
Metabolism	MetaCyc: POLR2A
	HUMANCyc: POLR2A
Regulation	Ensembl's Regulation: ENSG00000181222
	miRBase: chr17 :7,387,697-7,417,935
	TargetScan: NM_000937
	cisRED: ENSG00000181222
Context	iHOP: POLR2A
	cancer metabolism search in PubMed: POLR2A
	UCL Cancer Institute: POLR2A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for POLR2A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: POLR2A
	Familial Cancer Database: POLR2A

* 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	180660; gene+phenotype.
Orphanet
Disease	KEGG Disease: POLR2A
	MedGen: POLR2A (Human Medical Genetics with Condition)
	ClinVar: POLR2A
Phenotype	MGI: POLR2A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: POLR2A

Mutations for POLR2A

* 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
pancreas	POLR2A	chr17	7412656	7412676	ZBTB4	chr17	7383899	7383919

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 POLR2A 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
BE819347	NUP188	3	151	9	131768587	131768868	POLR2A	138	287	17	7407022	7411630
BF805544	CEP250	1	236	20	34092642	34095612	POLR2A	230	538	17	7416611	7416919
DA107051	GPM6A	1	248	4	176622745	176733415	POLR2A	249	581	17	7404138	7404883
BI061851	IKZF1	1	162	7	50424791	50424953	POLR2A	151	344	17	7404378	7404893
BF514571	POLR2A	18	79	17	7400767	7400828	POLR2A	74	285	17	7401012	7401430
BF512093	POLR2A	18	79	17	7400767	7400828	POLR2A	74	285	17	7401012	7401430
BI059477	IKZF1	1	162	7	50424791	50424953	POLR2A	151	344	17	7404378	7404893
BE833427	USP12	5	28	13	27666061	27666087	POLR2A	18	258	17	7416128	7416459
BE819348	NUP188	13	176	9	131768570	131768868	POLR2A	163	312	17	7407022	7411630
BI022194	AP2B1	1	211	17	33951591	33953833	POLR2A	203	437	17	7403972	7404297
BE159844	POLR2A	39	60	17	7409231	7409252	PVRL2	45	382	19	45376694	45377031

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

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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=108)	Stat. for Synonymous SNVs (# total SNVs=48)

Stat. for Deletions (# total SNVs=6)	Stat. for Insertions (# total SNVs=1)

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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
chr17:7416599-7416599	p.S1672S	4
chr17:7412911-7412911	p.R1258H	3
chr17:7405316-7405316	p.G816V	3
chr17:7399866-7399866	p.G157G	3
chr17:7401440-7401440	p.A416T	3
chr17:7414612-7414612	p.L1298L	2
chr17:7402441-7402441	p.R473R	2
chr17:7403970-7403970	p.N562D	2
chr17:7414731-7414731	p.M1309V	2
chr17:7416821-7416821	p.P1746P	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		5	1	17	2		11		7	2		14	4	1	1		18	18	1	16
# mutation		5	1	17	2		11		7	2		15	4	1	1		22	22	1	28
nonsynonymous SNV		4		11	1		9		6	2		10	3		1		13	17	1	20
synonymous SNV		1	1	6	1		2		1			5	1	1			9	5		8

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
chr17:7399844	p.G150D	3
chr17:7401440	p.A416T	3
chr17:7417451	p.R1603H	2
chr17:7404318	p.C451C	2
chr17:7416821	p.T647T	2
chr17:7402375	p.R475H	2
chr17:7416391	p.L1956L	2
chr17:7402446	p.P1746P	2
chr17:7405890	p.P1963Q	1
chr17:7415644	p.E683G	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 POLR2A 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 POLR2A

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


ANKFY1,ANKHD1-EIF4EBP3,ARID1A,BAZ2A,BCOR,CTC1,C9orf129, CYB5D1,DNAJC16,FRY,GIGYF2,HEATR5B,KDM3B,NCOR1, POLR2A,PRPF8,RABEP1,SPG11,THRAP3,TP53BP1,ZBTB4	ARID1A,BRPF3,C2CD3,COL4A5,EP400,KIAA0556,KIAA1217, KIAA1549,MAML1,MAP3K9,MDC1,POLR2A,SIPA1L1,SIPA1L3, SRCAP,TRRAP,TTLL5,YLPM1,ZNF135,ZNF142,ZSWIM5

ALKBH5,ANKFY1,ARID1A,C17orf85,CAMTA2,FLII,FXR2, KDM6B,NCOR1,PAFAH1B1,POLR2A,PRPF8,RABEP1,RAI1, SMG6,THRAP3,TNRC6B,TOP3A,WDR7,ZCCHC2,ZNF407	ACIN1,ANKRD52,BAZ2A,EP300,GBF1,GOLGA3,GTF3C1, HTT,KDM2A,KIAA2018,KMT2B___KMT2D,MYH9,NCOA6,PCNT, POLR2A,SMARCA4,SPEN,SRCAP,TCF20,TRRAP,UBR4

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 POLR2A

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P24928; -.
Chemistry	ChEMBL	CHEMBL1641353; -.
Organism-specific databases	PharmGKB	PA33507; -.
Organism-specific databases	CTD	5430; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00269	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Chlorotrianisene
DB00286	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Conjugated Estrogens
DB00255	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Diethylstilbestrol
DB00783	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved; investigational	Estradiol
DB00655	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Estrone
DB00977	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Ethinyl Estradiol
DB00890	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Dienestrol
DB00675	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Tamoxifen
DB00394	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Beclomethasone
DB00443	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Betamethasone
DB01222	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved; investigational	Budesonide
DB01410	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved; investigational	Ciclesonide
DB01260	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved; investigational	Desonide
DB01234	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved; investigational	Dexamethasone
DB00180	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved; investigational	Flunisolide
DB00588	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved; investigational	Fluticasone Propionate
DB00741	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Hydrocortisone
DB00959	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Methylprednisolone
DB00764	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Mometasone
DB01384	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Paramethasone
DB00860	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Prednisolone
DB00635	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Prednisone
DB00896	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Rimexolone
DB00620	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	approved	Triamcinolone

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Cross referenced IDs for POLR2A

* 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