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 POLR3A

Basic gene info.	Gene symbol	POLR3A
	Gene name	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa
	Synonyms	ADDH\|HLD7\|RPC1\|RPC155\|hRPC155
	Cytomap	UCSC genome browser: 10q22-q23
	Genomic location	chr10 :79734906-79789298
	Type of gene	protein-coding
	RefGenes	NM_007055.3,
	Ensembl id	ENSG00000148606
	Description	DNA-directed RNA polymerase III largest subunitDNA-directed RNA polymerase III subunit ADNA-directed RNA polymerase III subunit RPC1RNA polymerase III 155 kDa subunitRNA polymerase III subunit C1RNA polymerase III subunit C160RNA polymerase III subu
	Modification date	20141219
dbXrefs	MIM : 614258
	HGNC : HGNC
	Ensembl : ENSG00000148606
	HPRD : 17879
	Vega : OTTHUMG00000018550
Protein	UniProt: O14802 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_POLR3A
	BioGPS: 11128
	Gene Expression Atlas: ENSG00000148606
	The Human Protein Atlas: ENSG00000148606
Pathway	NCI Pathway Interaction Database: POLR3A
	KEGG: POLR3A
	REACTOME: POLR3A
	ConsensusPathDB
	Pathway Commons: POLR3A
Metabolism	MetaCyc: POLR3A
	HUMANCyc: POLR3A
Regulation	Ensembl's Regulation: ENSG00000148606
	miRBase: chr10 :79,734,906-79,789,298
	TargetScan: NM_007055
	cisRED: ENSG00000148606
Context	iHOP: POLR3A
	cancer metabolism search in PubMed: POLR3A
	UCL Cancer Institute: POLR3A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for POLR3A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: POLR3A
	Familial Cancer Database: POLR3A

* 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	607694; phenotype. 614258; gene.
Orphanet	77295; Odontoleukodystrophy. 88637; Hypomyelination - hypogonadotropic hypogonadism - hypodontia.
Disease	KEGG Disease: POLR3A
	MedGen: POLR3A (Human Medical Genetics with Condition)
	ClinVar: POLR3A
Phenotype	MGI: POLR3A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: POLR3A

Mutations for POLR3A

* 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	POLR3A	chr10	79761340	79761360	DLG5	chr10	79657335	79657355
ovary	POLR3A	chr10	79767002	79767022	DLG5	chr10	79616340	79616360
pancreas	POLR3A	chr10	79748622	79748642	DLG5	chr10	79616933	79616953

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 POLR3A related fusion information.

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

AI193375

PPM1F

210

22297586

22297795

POLR3A

202

487

79750804

79753117

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=79)	Stat. for Synonymous SNVs (# total SNVs=33)

Stat. for Deletions (# total SNVs=1)	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
chr10:79745903-79745903	p.F972L	3
chr10:79745850-79745850	p.N990S	2
chr10:79742503-79742503	p.H1168Y	2
chr10:79762001-79762001	p.L771L	2
chr10:79767484-79767484	p.A684P	2
chr10:79777462-79777462	p.Y434Y	2
chr10:79769648-79769648	p.R582C	2
chr10:79759756-79759756	p.E867*	2
chr10:79764506-79764506	p.Q739*	2
chr10:79739966-79739966	p.A1319A	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	4	5		16			7		6	2		19	3	2			13	15		13
# mutation	4	5		17			8		6	2		22	3	2			13	17		12
nonsynonymous SNV	4	3		13			6		6	2		15	1	1			3	14		4
synonymous SNV		2		4			2					7	2	1			10	3		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
chr10:79742042	p.A1210V	3
chr10:79769648	p.R582C	2
chr10:79745903	p.A32V	2
chr10:79785937	p.F972L	2
chr10:79773458	p.I901M	1
chr10:79784456	p.L668L	1
chr10:79741243	p.L471F	1
chr10:79752975	p.D311E	1
chr10:79778975	p.A1234V	1
chr10:79789149	p.L134L	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 POLR3A 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 POLR3A

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


AP3M1,DDX21,DLG5,FAM92A1P2,FUT11,GMCL1,GTF3C3, HSPD1,LOC650623,MAPK8,MOB4,PARG,POLR3A,RIF1, SF3B1,TFAM,UBXN7,UPF2,VCL,WAPAL,ZMIZ1	ADNP,ANKRD17,ARID1A,CDK13,CHD6,CHD7,CHD8, DHX33,GTF3C4,KDM3B,LMTK2,MDN1,MGA,N4BP2, NSD1,POLR3A,TP53BP1,TRRAP,TUBGCP4,ZNF776,ZNF827

ANAPC1,AP3M1,ASXL2,DDX21,DLG5,EIF4G1,GTF3C4, LARP1,MDN1,KMT2B___KMT2D,KAT6B,NEU3,PDCD11,POLR1A, POLR3A,RAD54L2,RIF1,SHPRH,SNRNP200,TGFBRAP1,URB1	ANKRD17,BTAF1,FAM208B,CAD,CDK12,DDI2,IKBKAP, ILF3,KIAA1244,LARP1,MDN1,KMT2B___KMT2D,POLR1A,POLR3A, RBM19,RC3H2,POMK,TUBGCP4,USP24,VPRBP,ZNF142

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 POLR3A

There's no related Drug.

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Cross referenced IDs for POLR3A

* 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