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 POLR2H

Basic gene info.	Gene symbol	POLR2H
	Gene name	polymerase (RNA) II (DNA directed) polypeptide H
	Synonyms	RPABC3\|RPB17\|RPB8
	Cytomap	UCSC genome browser: 3q28
	Genomic location	chr3 :184081193-184086363
	Type of gene	protein-coding
	RefGenes	NM_001278698.1, NM_001278699.1,NM_001278700.1,NM_001278714.1,NM_001278715.1, NM_006232.3,
	Ensembl id	ENSG00000163882
	Description	DNA-directed RNA polymerase II subunit HDNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptideDNA-directed RNA polymerases I, II, and III subunit RPABC3RPB8 homolog
	Modification date	20141207
dbXrefs	MIM : 606023
	HGNC : HGNC
	Ensembl : ENSG00000163882
	HPRD : 09082
	Vega : OTTHUMG00000156746
Protein	UniProt: P52434 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_POLR2H
	BioGPS: 5437
	Gene Expression Atlas: ENSG00000163882
	The Human Protein Atlas: ENSG00000163882
Pathway	NCI Pathway Interaction Database: POLR2H
	KEGG: POLR2H
	REACTOME: POLR2H
	ConsensusPathDB
	Pathway Commons: POLR2H
Metabolism	MetaCyc: POLR2H
	HUMANCyc: POLR2H
Regulation	Ensembl's Regulation: ENSG00000163882
	miRBase: chr3 :184,081,193-184,086,363
	TargetScan: NM_001278698
	cisRED: ENSG00000163882
Context	iHOP: POLR2H
	cancer metabolism search in PubMed: POLR2H
	UCL Cancer Institute: POLR2H
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for POLR2H(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: POLR2H
	Familial Cancer Database: POLR2H

* 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	606023; gene.
Orphanet
Disease	KEGG Disease: POLR2H
	MedGen: POLR2H (Human Medical Genetics with Condition)
	ClinVar: POLR2H
Phenotype	MGI: POLR2H (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: POLR2H

Mutations for POLR2H

* 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 POLR2H 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
BF001934	POLR2H	5	349	3	184086046	184086367	DTX3L	342	522	3	122291997	122292177
AI680578	POLR2H	21	85	3	184086267	184086331	SRRT	82	351	7	100485876	100486235

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=10)	Stat. for Synonymous SNVs (# total SNVs=4)

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
chr3:184086011-184086011	p.D128N	1
chr3:184084506-184084506	p.A85S	1
chr3:184086028-184086028	p.H133Q	1
chr3:184081293-184081293	p.L5L	1
chr3:184084507-184084507	p.A85G	1
chr3:184081335-184081335	p.G19S	1
chr3:184084584-184084584	p.R111C	1
chr3:184081350-184081350	p.R24*	1
chr3:184084585-184084585	p.R111H	1
chr3:184082777-184082777	p.E33K	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			5	1				1			2
# mutation		1		2					1			5	1				1			2
nonsynonymous SNV		1		2								3	1				1			2
synonymous SNV									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
chr3:184086008	p.L5L,POLR2H	1
chr3:184081293	p.G19S,POLR2H	1
chr3:184086028	p.E33K,POLR2H	1
chr3:184081335	p.L39V,POLR2H	1
chr3:184086079	p.L70V,POLR2H	1
chr3:184082777	p.N76N,POLR2H	1
chr3:184082795	p.P77P,POLR2H	1
chr3:184082971	p.R84S,POLR2H	1
chr3:184082991	p.R111H,POLR2H	1
chr3:184082994	p.L94F,POLR2H	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 POLR2H 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 POLR2H

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


ABCF3,ALG3,AP2M1,C19orf43,C1orf35,ECE2,LOC152217, LSM4,LSM7,MRPL47,MRPL55,NDUFA11,PARL,POLR2H, PSMG3,RFXANK,RPL35A,RPP21,SNRPA,SNRPD2,USMG5	SYNE4,CCDC24,COQ4,DPCD,FBXW9,LOC92659,LPAR2, LYPLA2,NMRAL1,NR2C2AP,PAFAH1B3,POLR2H,PPAP2C,PRCC, SLC35C2,STAP2,TARBP2,TMEM198,TSEN34,TSEN54,WDR34

UQCC2,C9orf142,CCDC58,TMA7,ECE2,GADD45GIP1,MRPL14, MRPL17,NDUFB4,NDUFS3,NR2C2AP,PARL,PCGF1,POLR2H, RFC4,RPL24,RPL32,RPL35,RPL35A,SNHG1,SS18L2	ALG14,ATP6V0B,AUP1,MIEN1,PLGRKT,CCL15,CIB1, CLIC1,GEMIN8P4,H2AFY,LGALS3,MLX,PDCD6,PLEKHJ1, POLR2H,RASSF7,VIMP,TMEM106C,TRAF4,TSG101,VPS25

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 POLR2H

There's no related Drug.

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Cross referenced IDs for POLR2H

* 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