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 POLR3C

Basic gene info.	Gene symbol	POLR3C
	Gene name	polymerase (RNA) III (DNA directed) polypeptide C (62kD)
	Synonyms	RPC3\|RPC62
	Cytomap	UCSC genome browser: 1q21.1
	Genomic location	chr1 :145592604-145610884
	Type of gene	protein-coding
	RefGenes	NM_006468.6,
	Ensembl id	ENSG00000264806
	Description	DNA-directed III 62 kDa polypeptideDNA-directed RNA polymerase III subunit CDNA-directed RNA polymerase III subunit RPC3RNA polymerase III 62 kDa subunitRNA polymerase III subunit C3
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000186141
	HPRD : 17880
	Vega : OTTHUMG00000013753
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_POLR3C
	BioGPS: 10623
	Gene Expression Atlas: ENSG00000264806
	The Human Protein Atlas: ENSG00000264806
Pathway	NCI Pathway Interaction Database: POLR3C
	KEGG: POLR3C
	REACTOME: POLR3C
	ConsensusPathDB
	Pathway Commons: POLR3C
Metabolism	MetaCyc: POLR3C
	HUMANCyc: POLR3C
Regulation	Ensembl's Regulation: ENSG00000264806
	miRBase: chr1 :145,592,604-145,610,884
	TargetScan: NM_006468
	cisRED: ENSG00000264806
Context	iHOP: POLR3C
	cancer metabolism search in PubMed: POLR3C
	UCL Cancer Institute: POLR3C
Assigned class in ccmGDB	C

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Phenotypic Information for POLR3C(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: POLR3C
	Familial Cancer Database: POLR3C

* 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: POLR3C
	MedGen: POLR3C (Human Medical Genetics with Condition)
	ClinVar: POLR3C
Phenotype	MGI: POLR3C (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: POLR3C

Mutations for POLR3C

* 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	POLR3C	chr1	145600642	145600662	TXNIP	chr1	145441422	145441442

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 POLR3C 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
BF335120	POLR3C	16	255	1	145605925	145606165	POLR3C	247	390	1	145606173	145606316
W23948	BRK1	2	228	3	10157452	10168040	POLR3C	215	445	1	145601551	145606321
BI027593	POLR3C	1	156	1	145601562	145601839	POLR3C	155	229	1	145598536	145598610

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=32)	Stat. for Synonymous SNVs (# total SNVs=10)

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
chr1:145608133-145608133	p.Y188Y	3
chr1:145594051-145594051	p.R504H	3
chr1:145594076-145594076	p.R496C	3
chr1:145608468-145608468	p.N113N	2
chr1:145608488-145608488	p.V107I	2
chr1:145608566-145608566	p.R81W	2
chr1:145601595-145601595	p.L271I	2
chr1:145592758-145592758	p.E513K	2
chr1:145601614-145601614	p.S264S	2
chr1:145601821-145601821	p.A237G	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	3	2		4	2				1			4	1	3			2	3		7
# mutation	3	2		4	2				1			8	1	3			2	3		7
nonsynonymous SNV	1	2		4	1				1			5		1			2	2		4
synonymous SNV	2				1							3	1	2				1		3

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
chr1:145594051	p.R504H	3
chr1:145594076	p.S264S	2
chr1:145601614	p.G232W	2
chr1:145601837	p.R496C	2
chr1:145608142	p.I491I	1
chr1:145598565	p.P213P	1
chr1:145608189	p.A469S	1
chr1:145594089	p.L195L	1
chr1:145598609	p.S464S	1
chr1:145608196	p.P191L	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 POLR3C 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 POLR3C

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


ANP32E,APH1A,CHD1L,CRTC2,DAP3,GATAD2B,GPR89A, ILF2,MRPL9,PEX11B,PI4KB,PIP5K1A,POLR3C,PRCC, PRUNE,RBM8A,RNF115,SCNM1,SETDB1,SF3B4,VPS72	BTF3,ZFAS1,EIF3D,GNB2L1,NACA,EPB41L4A-AS1,NPM1, POLR3C,RPL11,RPL22,RPL4,RPL5,RPL6,RPL7, RPS18,RPS27A,RPS3A,RPS4X,RPS6,RPS7,SF3A3

ACBD6,DIEXF,C1orf43,DAP3,DEDD,MRPL9,NUP133, NVL,POLR3C,PRUNE,RBM34,RFWD2,RNF115,RRP15, TADA1,TBCE,TFB2M,TIPRL,TOMM20,UFC1,VPS72	C12orf10,DRG2,EIF3M,GNB2L1,PEMT,POLR3C,RNMTL1, RPL10,RPL10A,RPL12,RPL18,RPL19,RPL30,RPL32, RPL3,RPL7,RPL7A,RPUSD4,RSL1D1,TOMM20,WDR74

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 POLR3C

There's no related Drug.

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Cross referenced IDs for POLR3C

* 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