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 POLE2

Basic gene info.	Gene symbol	POLE2
	Gene name	polymerase (DNA directed), epsilon 2, accessory subunit
	Synonyms	DPE2
	Cytomap	UCSC genome browser: 14q21-q22
	Genomic location	chr14 :50116898-50155098
	Type of gene	protein-coding
	RefGenes	NM_001197330.1, NM_001197331.1,NM_002692.3,
	Ensembl id	ENSG00000100479
	Description	DNA polymerase II subunit 2DNA polymerase epsilon subunit 2DNA polymerase epsilon subunit Bpolymerase (DNA directed), epsilon 2 (p59 subunit)
	Modification date	20141207
dbXrefs	MIM : 602670
	HGNC : HGNC
	Ensembl : ENSG00000100479
	HPRD : 16007
	Vega : OTTHUMG00000170813
Protein	UniProt: P56282 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_POLE2
	BioGPS: 5427
	Gene Expression Atlas: ENSG00000100479
	The Human Protein Atlas: ENSG00000100479
Pathway	NCI Pathway Interaction Database: POLE2
	KEGG: POLE2
	REACTOME: POLE2
	ConsensusPathDB
	Pathway Commons: POLE2
Metabolism	MetaCyc: POLE2
	HUMANCyc: POLE2
Regulation	Ensembl's Regulation: ENSG00000100479
	miRBase: chr14 :50,116,898-50,155,098
	TargetScan: NM_001197330
	cisRED: ENSG00000100479
Context	iHOP: POLE2
	cancer metabolism search in PubMed: POLE2
	UCL Cancer Institute: POLE2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for POLE2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: POLE2
	Familial Cancer Database: POLE2

* 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	602670; gene.
Orphanet
Disease	KEGG Disease: POLE2
	MedGen: POLE2 (Human Medical Genetics with Condition)
	ClinVar: POLE2
Phenotype	MGI: POLE2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: POLE2

Mutations for POLE2

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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	POLE2	chr14	50124682	50124702	LRR1	chr14	50078557	50078577
ovary	POLE2	chr14	50124684	50124704	LRR1	chr14	50078557	50078577
ovary	POLE2	chr14	50124691	50124711	LRR1	chr14	50078565	50078585
pancreas	POLE2	chr14	50126261	50126281	POLE2	chr14	50126324	50126344

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 POLE2 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

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=22)	Stat. for Synonymous SNVs (# total SNVs=13)

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
chr14:50117145-50117145	p.I445M	3
chr14:50140860-50140860	p.R133Q	2
chr14:50120778-50120778	p.L381F	2
chr14:50118023-50118023	p.V428V	2
chr14:50122404-50122404	p.R305C	2
chr14:50146467-50146467	p.C74F	2
chr14:50133134-50133134	p.?	2
chr14:50150360-50150360	p.E40D	1
chr14:50118061-50118061	p.R416C	1
chr14:50130032-50130032	p.?	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=2

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		6	1		2		2		1	1	1	2			2	5		4
# mutation	3	2		7	1		2		2		1	1	1	2			2	5		4
nonsynonymous SNV	1	1		5	1		1		1			1	1	2			2	4		3
synonymous SNV	2	1		2			1		1		1							1		1

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
chr14:50117145	p.R107Q,POLE2	2
chr14:50140860	p.R279C,POLE2	2
chr14:50118023	p.I419I,POLE2	2
chr14:50122404	p.V402V,POLE2	2
chr14:50136312	p.I386L,POLE2	1
chr14:50122474	p.T115N,POLE2	1
chr14:50118020	p.L355F,POLE2	1
chr14:50131378	p.P354S,POLE2	1
chr14:50140867	p.R105C,POLE2	1
chr14:50131391	p.P339S,POLE2	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 POLE2 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 POLE2

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


CCNB1,CDKN3,DLGAP5,ERCC6L,GINS1,HELLS,KIF11, KIF4A,LMNB1,NCAPG,NCAPH,OIP5,PARP2,PCNA, POLE2,LRR1,SCAF11___GEMIN2___ZEB2,SPC25,TPX2,VRK1,WDHD1	PARPBP,CENPH,CENPK,E2F5,FANCD2,FANCI,FBXO5, GINS1,GINS4,HELLS,KIF18A,MAD2L1,PAICS,PLK4, POLE2,RFC3,SRPK1,STIL,TDP1,ZNF93,ZWILCH

ASF1B,EFCAB11,CDCA4,CDKN3,CHEK1,DLGAP5,EIF2S1, ERH,FANCM,MCM6,MTHFD1,NCAPH,PARP2,POLE2, LRR1,PRIM1,PSMA3,RFC4,RFC5,VRK1,WDHD1	DDIAS,DBF4,EIF4A1,EIF5AL1,GINS1,GINS2,H2AFZ, HNRNPF,KIAA0101,NME1,PCNA,POLE2,PSMD14,RAD51AP1, RAN,RANBP1,RFC3,RFC4,SNRPD1,UBE2T,VRK1

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 POLE2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA278; -.
Organism-specific databases	CTD	5427; -.

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
DB00242	polymerase (DNA directed), epsilon 2, accessory subunit	approved; investigational	Cladribine
DB01050	polymerase (DNA directed), epsilon 2, accessory subunit	approved	Ibuprofen

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Cross referenced IDs for POLE2

* 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