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 POLE

Basic gene info.	Gene symbol	POLE
	Gene name	polymerase (DNA directed), epsilon, catalytic subunit
	Synonyms	CRCS12\|FILS\|POLE1
	Cytomap	UCSC genome browser: 12q24.3
	Genomic location	chr12 :133200347-133263945
	Type of gene	protein-coding
	RefGenes	NM_006231.3,
	Ensembl id	ENSG00000177084
	Description	DNA polymerase II subunit ADNA polymerase epsilon catalytic subunit A
	Modification date	20141207
dbXrefs	MIM : 174762
	HGNC : HGNC
	Ensembl : ENSG00000177084
	HPRD : 07177
	Vega : OTTHUMG00000168045
Protein	UniProt: Q07864 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_POLE
	BioGPS: 5426
	Gene Expression Atlas: ENSG00000177084
	The Human Protein Atlas: ENSG00000177084
Pathway	NCI Pathway Interaction Database: POLE
	KEGG: POLE
	REACTOME: POLE
	ConsensusPathDB
	Pathway Commons: POLE
Metabolism	MetaCyc: POLE
	HUMANCyc: POLE
Regulation	Ensembl's Regulation: ENSG00000177084
	miRBase: chr12 :133,200,347-133,263,945
	TargetScan: NM_006231
	cisRED: ENSG00000177084
Context	iHOP: POLE
	cancer metabolism search in PubMed: POLE
	UCL Cancer Institute: POLE
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer Description
Cancer	CGAP: POLE
	Familial Cancer Database: POLE

* 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 UCEC ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_PURINE_METABOLISM KEGG_PYRIMIDINE_METABOLISM

Others
OMIM	174762; gene. 615083; phenotype. 615139; phenotype.
Orphanet	352712; Facial dysmorphism - immunodeficiency - livedo - short stature.
Disease	KEGG Disease: POLE
	MedGen: POLE (Human Medical Genetics with Condition)
	ClinVar: POLE
Phenotype	MGI: POLE (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: POLE

Mutations for POLE

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	POLE	chr12	133202263	133202283		chr12	59759771	59759791
ovary	POLE	chr12	133259196	133259216	PGAM5	chr12	133287796	133287816
pancreas	POLE	chr12	133219226	133219246	POLE	chr12	133219321	133219341

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 POLE 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
AB209902	POLE	1	3576	12	133225513	133254307	HMGCL	3572	5067	1	24128377	24147086
BG986284	POLE	3	181	12	133208986	133209317	ADM	177	321	11	10328411	10328555

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=16

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=190)	Stat. for Synonymous SNVs (# total SNVs=46)

Stat. for Deletions (# total SNVs=4)	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
chr12:133253184-133253184	p.P286R	15
chr12:133250289-133250289	p.V411L	9
chr12:133220532-133220532	p.V1394A	4
chr12:133244137-133244137	p.T757T	3
chr12:133250250-133250250	p.L424I	3
chr12:133215787-133215787	p.R1826W	2
chr12:133219481-133219481	p.H1551H	2
chr12:133249319-133249319	p.L527P	2
chr12:133256230-133256230	p.H144R	2
chr12:133233743-133233743	p.F1187F	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=10

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	6	9		35			8		3			23	9	3		1	22	20	2	31
# mutation	7	9		37			9		3			32	9	3		1	23	27	2	49
nonsynonymous SNV	6	7		31			6		3			26	6	2			12	19	1	35
synonymous SNV	1	2		7			3					6	3	1		1	11	8	1	14

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
chr12:133253184	p.P286H	10
chr12:133250289	p.V411L	8
chr12:133220532	p.V1394A	4
chr12:133253151	p.S297F	3
chr12:133250250	p.L424V	3
chr12:133219468	p.L1235I	2
chr12:133242025	p.Y1889C	2
chr12:133226355	p.E1715K	2
chr12:133234500	p.R1879C	2
chr12:133220438	p.A456P	2

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 POLE 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 POLE

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


ANAPC11,AP2S1,C19orf24,C19orf70,CHCHD5,COMMD4,FDX1L, GADD45GIP1,JOSD2,MRPL53,LINC00116,NDUFA11,NDUFA13,NDUFB2, NDUFB7,POLE4,RNF181,RPS19BP1,TIMM13,TMEM160,UQCR11	ATP5E,ATP6V0E1,ATP6V1F,MINOS1,BRK1,CAPNS1,DYNLRB1, KRTCAP2,MGST2,NEDD8,NOP10,OST4,PKIG,POLE4, RBX1,RNASEK,RNF181,SERF2,SRP14,TAF10,VKORC1

ANAPC11,UQCC3,ATRAID,PTRHD1,C7orf55,DTYMK,ISCA2, MRPL11,MRPS28,MYEOV2,LINC00116,NDUFB1,NDUFB2,NDUFB7, OST4,POLE4,SIVA1,STRA13,PAM16,TIMM8B,UQCR11	ATP5O,BUD31,COX14,CAPZA2,COMMD3,FIS1,GOLGA7, NDUFA11,NDUFA13,NDUFA8,NDUFB7,NDUFS4,NFU1,PEX2, POLE4,SRP14,SUPT4H1,TMEM14C,TRAPPC3,UQCR11,ZNF410

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 POLE

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2363042; -.
Organism-specific databases	PharmGKB	PA277; -.
Organism-specific databases	CTD	5426; -.

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, catalytic subunit	approved; investigational	Cladribine
DB01033	polymerase (DNA directed), epsilon, catalytic subunit	approved	Mercaptopurine
DB00563	polymerase (DNA directed), epsilon, catalytic subunit	approved	Methotrexate
DB00441	polymerase (DNA directed), epsilon, catalytic subunit	approved	Gemcitabine

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Cross referenced IDs for POLE

* 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