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 POLD1

Basic gene info.	Gene symbol	POLD1
	Gene name	polymerase (DNA directed), delta 1, catalytic subunit
	Synonyms	CDC2\|CRCS10\|MDPL\|POLD
	Cytomap	UCSC genome browser: 19q13.3
	Genomic location	chr19 :50887579-50921275
	Type of gene	protein-coding
	RefGenes	NM_001256849.1, NM_002691.3,NR_046402.1,
	Ensembl id	ENSG00000062822
	Description	CDC2 homologDNA polymerase delta catalytic subunitDNA polymerase subunit delta p125polymerase (DNA directed), delta 1, catalytic subunit 125kDa
	Modification date	20141207
dbXrefs	MIM : 174761
	HGNC : HGNC
	Ensembl : ENSG00000062822
	HPRD : 08882
	Vega : OTTHUMG00000183037
Protein	UniProt: P28340 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_POLD1
	BioGPS: 5424
	Gene Expression Atlas: ENSG00000062822
	The Human Protein Atlas: ENSG00000062822
Pathway	NCI Pathway Interaction Database: POLD1
	KEGG: POLD1
	REACTOME: POLD1
	ConsensusPathDB
	Pathway Commons: POLD1
Metabolism	MetaCyc: POLD1
	HUMANCyc: POLD1
Regulation	Ensembl's Regulation: ENSG00000062822
	miRBase: chr19 :50,887,579-50,921,275
	TargetScan: NM_001256849
	cisRED: ENSG00000062822
Context	iHOP: POLD1
	cancer metabolism search in PubMed: POLD1
	UCL Cancer Institute: POLD1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of POLD1 in cancer cell metabolism	1. Mertz TM, Sharma S, Chabes A, Shcherbakova PV (2015) Colon cancer-associated mutator DNA polymerase δ variant causes expansion of dNTP pools increasing its own infidelity. Proceedings of the National Academy of Sciences 112: E2467-E2476. go to article

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Phenotypic Information for POLD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: POLD1
	Familial Cancer Database: POLD1

* 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	174761; gene. 612591; phenotype. 615381; phenotype.
Orphanet	363649; Mandibular hypoplasia-deafness-progeroid syndrome.
Disease	KEGG Disease: POLD1
	MedGen: POLD1 (Human Medical Genetics with Condition)
	ClinVar: POLD1
Phenotype	MGI: POLD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: POLD1

Mutations for POLD1

* 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 POLD1 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=70)	Stat. for Synonymous SNVs (# total SNVs=26)

Stat. for Deletions (# total SNVs=5)	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
chr19:50918720-50918720	p.A864T	3
chr19:50906815-50906815	p.F401F	3
chr19:50912086-50912086	p.Y607C	2
chr19:50918097-50918097	p.S805N	2
chr19:50916686-50916686	p.V720I	2
chr19:50905055-50905055	p.P116fs*53	2
chr19:50909504-50909504	p.F436L	2
chr19:50906786-50906786	p.V392M	2
chr19:50905959-50905959	p.R311C	2
chr19:50905595-50905595	p.F241F	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=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	1	1	1	18	1		4		3			4	3	2		1	13	11		14
# mutation	1	1	1	17	1		4		3			5	3	2		1	14	12		16
nonsynonymous SNV	1	1		12	1		3		2			4	2			1	6	8		11
synonymous SNV			1	5			1		1			1	1	2			8	4		5

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
chr19:50906815	p.F401F,POLD1	2
chr19:50918720	p.A864T,POLD1	2
chr19:50905959	p.F241F,POLD1	2
chr19:50917112	p.Q461H,POLD1	2
chr19:50909579	p.S788S,POLD1	2
chr19:50905595	p.R311C,POLD1	2
chr19:50906786	p.A145D,POLD1	2
chr19:50905152	p.V392M,POLD1	2
chr19:50918719	p.F637L,POLD1	1
chr19:50919778	p.A860A,POLD1	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 POLD1 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 POLD1

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


ATAD3A,BAX,BCL2L12,C19orf48,CCDC124,CDT1,CPSF4, CTU1,DAZAP1,IRF3,LIG1,MCM5,MCM7,MXD3, NUP62,PKMYT1,POLD1,PPAN,PRMT1,TCOF1,UBE2S	ARVCF,AXIN1,C17orf70,CC2D1A,CHERP,CHTF18,EHMT2, FBXL19,GRK6,MCM5,POLD1,PUS1,RIN1,SLC12A9, SNAPC4,SPPL2B,TCF3,TRAF2,TSC22D4,U2AF2,ZMYND19

BCL2L12,C16orf59,C17orf53,CDT1,CHAF1A,KIF18B,LIG1, LMNB2,MCM2,PKMYT1,POLD1,POLE,PRPF31,RAD54L, RUVBL2,TACC3,THOP1,TOMM40,TRIM28,UHRF1,WDR62	C14orf80,CDT1,CHAF1A,CHTF18,H2AFX,LIG1,LOC100128191, LRRC45,MCM5,MED24,TONSL,POLD1,PPP2R3B,RECQL4, REEP4,SPC24,SYMPK,TACC3,TARS2,U2AF2,ZNF296

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 POLD1

There's no related Drug.

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Cross referenced IDs for POLD1

* 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