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 EDC3

Basic gene info.	Gene symbol	EDC3
	Gene name	enhancer of mRNA decapping 3
	Synonyms	LSM16\|YJDC\|YJEFN2
	Cytomap	UCSC genome browser: 15q24.1
	Genomic location	chr15 :74922898-74988386
	Type of gene	protein-coding
	RefGenes	NM_001142443.1, NM_001142444.1,NM_025083.3,
	Ensembl id	ENSG00000179151
	Description	LSM16 homolog (EDC3, S. cerevisiae)enhancer of mRNA decapping 3 homologenhancer of mRNA-decapping protein 3hYjeF_N2hYjeF_N2-15q23yjeF N-terminal domain-containing protein 2yjeF domain containingyjeF domain-containing protein 1yjeF_N2
	Modification date	20141207
dbXrefs	MIM : 609842
	HGNC : HGNC
	Ensembl : ENSG00000179151
	HPRD : 07954
	Vega : OTTHUMG00000142815
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EDC3
	BioGPS: 80153
	Gene Expression Atlas: ENSG00000179151
	The Human Protein Atlas: ENSG00000179151
Pathway	NCI Pathway Interaction Database: EDC3
	KEGG: EDC3
	REACTOME: EDC3
	ConsensusPathDB
	Pathway Commons: EDC3
Metabolism	MetaCyc: EDC3
	HUMANCyc: EDC3
Regulation	Ensembl's Regulation: ENSG00000179151
	miRBase: chr15 :74,922,898-74,988,386
	TargetScan: NM_001142443
	cisRED: ENSG00000179151
Context	iHOP: EDC3
	cancer metabolism search in PubMed: EDC3
	UCL Cancer Institute: EDC3
Assigned class in ccmGDB	C

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Phenotypic Information for EDC3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EDC3
	Familial Cancer Database: EDC3

* 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
Orphanet
Disease	KEGG Disease: EDC3
	MedGen: EDC3 (Human Medical Genetics with Condition)
	ClinVar: EDC3
Phenotype	MGI: EDC3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EDC3

Mutations for EDC3

* 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
breast	EDC3	chr15	74982147	74982147	SCAMP2	chr15	75139164	75139164

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 EDC3 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

BE095213

EDC3

303

74925314

74925601

EDC3

294

352

74925607

74925665

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=14)	Stat. for Synonymous SNVs (# total SNVs=14)

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
chr15:74964117-74964117	p.?	5
chr15:74948297-74948297	p.I199I	3
chr15:74948152-74948152	p.E248*	2
chr15:74932898-74932898	p.E295K	2
chr15:74948394-74948394	p.R167K	1
chr15:74964046-74964046	p.D78D	1
chr15:74925269-74925269	p.V404E	1
chr15:74963798-74963798	p.S161F	1
chr15:74964059-74964059	p.Q74R	1
chr15:74927761-74927761	p.S394F	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	3	2	2	4	1		1		2			2	1				5	2		5
# mutation	3	2	2	4	1		1		2			2	1				5	2		5
nonsynonymous SNV	2	1	2		1				2			1					4	1		1
synonymous SNV	1	1		4			1					1	1				1	1		4

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
chr15:74964022	p.V372V,EDC3	1
chr15:74927793	p.D122A,EDC3	1
chr15:74948373	p.Q115E,EDC3	1
chr15:74964112	p.L368L,EDC3	1
chr15:74927826	p.A113A,EDC3	1
chr15:74948394	p.N359N,EDC3	1
chr15:74967310	p.N98N,EDC3	1
chr15:74927838	p.P264P,EDC3	1
chr15:74963798	p.P86P,EDC3	1
chr15:74967365	p.S253S,EDC3	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 EDC3 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 EDC3

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


ANP32A,ARID3B,ARIH1,FAM219B,VWA9,EDC3,FAM103A1, FBXO22,HMG20A,IDH3A,IREB2,MORF4L1,NEO1,PDCD7, PTPN9,RCN2,SCAMP2,SIN3A,UBL7,WDR61,ZNF592	SNHG20,C1orf226,CAD,CCDC120,CCDC85C,CD3EAP,CLSTN1, DDX31,DKC1,EDC3,GEMIN4,LIG1,MKS1,NAT10, PDCD11,POLDIP3,PTK7,SETDB1,WDR6,ZNF346,ZNF74

ANP32A,ARIH1,ASB7,C15orf39,VWA9,CSK,EDC3, HMG20A,IREB2,LCMT2,FAN1,PDCD7,PTPN9,RFX7, RPAP1,SCAND2P,SIN3A,SNUPN,UBL7,ZNF592,ZSCAN29	ARHGEF10L,DIEXF,CDAN1,CNTROB,DPH1,EDC3,EIF2AK4, FLJ90757,INTS9,ITFG2,TTI1,LIMD1,MMS19,MTSS1, POGK,PTCD1,PTK7,RANBP10,SETDB1,NELFA,ZDHHC8

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 EDC3

There's no related Drug.

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Cross referenced IDs for EDC3

* 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