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 DCP2

Basic gene info.	Gene symbol	DCP2
	Gene name	decapping mRNA 2
	Synonyms	NUDT20
	Cytomap	UCSC genome browser: 5q22.2
	Genomic location	chr5 :112312406-112357892
	Type of gene	protein-coding
	RefGenes	NM_001242377.1, NM_152624.5,NR_038352.1,
	Ensembl id	ENSG00000172795
	Description	DCP2 decapping enzyme homologhDpcm7GpppN-mRNA hydrolasemRNA-decapping enzyme 2nudix (nucleoside diphosphate linked moiety X)-type motif 20
	Modification date	20141207
dbXrefs	MIM : 609844
	HGNC : HGNC
	Ensembl : ENSG00000172795
	HPRD : 13125
	Vega : OTTHUMG00000162853
Protein	UniProt: Q8IU60 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_DCP2
	BioGPS: 167227
	Gene Expression Atlas: ENSG00000172795
	The Human Protein Atlas: ENSG00000172795
Pathway	NCI Pathway Interaction Database: DCP2
	KEGG: DCP2
	REACTOME: DCP2
	ConsensusPathDB
	Pathway Commons: DCP2
Metabolism	MetaCyc: DCP2
	HUMANCyc: DCP2
Regulation	Ensembl's Regulation: ENSG00000172795
	miRBase: chr5 :112,312,406-112,357,892
	TargetScan: NM_001242377
	cisRED: ENSG00000172795
Context	iHOP: DCP2
	cancer metabolism search in PubMed: DCP2
	UCL Cancer Institute: DCP2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of DCP2 in cancer cell metabolism	1. Grudzien-Nogalska E, Jemielity J, Kowalska J, Darzynkiewicz E, Rhoads RE (2007) Phosphorothioate cap analogs stabilize mRNA and increase translational efficiency in mammalian cells. RNA 13: 1745-1755. doi: 10.1261/rna.701307. pmid: 1986804. go to article 2. Mencia N, Selga E, Noe V, Ciudad CJ (2011) Underexpression of miR-224 in methotrexate resistant human colon cancer cells. Biochem Pharmacol 82: 1572-1582. doi: 10.1016/j.bcp.2011.08.009. go to article

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Phenotypic Information for DCP2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: DCP2
	Familial Cancer Database: DCP2

* 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
REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	609844; gene.
Orphanet
Disease	KEGG Disease: DCP2
	MedGen: DCP2 (Human Medical Genetics with Condition)
	ClinVar: DCP2
Phenotype	MGI: DCP2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: DCP2

Mutations for DCP2

* 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	DCP2	chr5	112337257	112337277		chr5	112002066	112002086
ovary	DCP2	chr5	112345642	112345662	DCP2	chr5	112342280	112342300
pancreas	DCP2	chr5	112332702	112332722	SRP19	chr5	112224571	112224591

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 DCP2 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
AK025019	KLF11	2	61	2	10193819	10193878	DCP2	61	2511	5	112354215	112356667
CA945240	DCP2	1	220	5	112356465	112357100	DCP2	213	308	5	112356368	112356463
CB852569	DCP2	21	226	5	112320135	112320344	DCP2	221	369	5	112320003	112320151

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=34)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr5:112327832-112327832	p.P74T	2
chr5:112337369-112337369	p.L268L	2
chr5:112336808-112336808	p.K154E	2
chr5:112339641-112339641	p.R270Q	2
chr5:112346489-112346489	p.D362Y	2
chr5:112321534-112321534	p.R19Q	2
chr5:112337364-112337364	p.K267E	1
chr5:112343727-112343727	p.Q345Q	1
chr5:112336802-112336802	p.D152Y	1
chr5:112343733-112343733	p.S347S	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=1

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	2			7			1					1				1	5	6		13
# mutation	2			7			1					1				1	5	6		13
nonsynonymous SNV	2			5			1									1	4	4		10
synonymous SNV				2								1					1	2		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
chr5:112343668	p.H304Y,DCP2	1
chr5:112327847	p.K133T,DCP2	1
chr5:112337151	p.M318I	1
chr5:112343727	p.E135D,DCP2	1
chr5:112328378	p.G320E	1
chr5:112337338	p.A136T,DCP2	1
chr5:112343733	p.Y326H	1
chr5:112328433	p.D152Y,DCP2	1
chr5:112337364	p.Q345Q	1
chr5:112346470	p.R173C,DCP2	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 DCP2 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 DCP2

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


APC,C5orf24,CSNK1G3,DCP2,DMXL1,ERBB2IP,FAM13B, LYSMD3,MATR3,MFAP3,MIER3,PPIP5K2,RBM27,SAP30L, SLC25A46,SMAD5,SRFBP1,TNPO1,TRIM23,WDR36,YTHDC2	CNOT6,DCP2,LSM11,RBM12B,SPIN4,TRIM59,ZBTB33, ZFP14,ZFP62,ZNF223,ZNF235,ZNF253,ZNF260,ZNF264, ZNF286A,ZNF525,ZNF529,ZNF681,ZNF709,ZNF780A,ZNF84

ANKRD32,APC,BDP1,CEP120,CHD1,CNOT6,DCP2, DDX46,DMXL1,FBXW11,FER,GXYLT1,NSD1,PHAX, PIKFYVE,SRP19,TRIM23,WDFY2,WDR36,YTHDC2,ZFYVE16	AIM1,CSNK1G1,CSNK2A1,DCP2,DNMT3B,FAM117B,HARS2, KDM4A,NAPEPLD,NLK,OSBP,PANK2,SPG11,SPTLC2, STK4,STRBP,TAF5,VCPIP1,WDFY1,ZNF217,ZNF490

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 DCP2

There's no related Drug.

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Cross referenced IDs for DCP2

* 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