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 ECHS1

Basic gene info.	Gene symbol	ECHS1
	Gene name	enoyl CoA hydratase, short chain, 1, mitochondrial
	Synonyms	SCEH
	Cytomap	UCSC genome browser: 10q26.2-q26.3
	Genomic location	chr10 :135175986-135186908
	Type of gene	protein-coding
	RefGenes	NM_004092.3,
	Ensembl id	ENSG00000127884
	Description	enoyl Coenzyme A hydratase, short chain, 1, mitochondrialenoyl-CoA hydratase 1enoyl-CoA hydratase, mitochondrialshort-chain enoyl-CoA hydratase
	Modification date	20141207
dbXrefs	MIM : 602292
	HGNC : HGNC
	Ensembl : ENSG00000127884
	HPRD : 03799
	Vega : OTTHUMG00000019320
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ECHS1
	BioGPS: 1892
	Gene Expression Atlas: ENSG00000127884
	The Human Protein Atlas: ENSG00000127884
Pathway	NCI Pathway Interaction Database: ECHS1
	KEGG: ECHS1
	REACTOME: ECHS1
	ConsensusPathDB
	Pathway Commons: ECHS1
Metabolism	MetaCyc: ECHS1
	HUMANCyc: ECHS1
Regulation	Ensembl's Regulation: ENSG00000127884
	miRBase: chr10 :135,175,986-135,186,908
	TargetScan: NM_004092
	cisRED: ENSG00000127884
Context	iHOP: ECHS1
	cancer metabolism search in PubMed: ECHS1
	UCL Cancer Institute: ECHS1
Assigned class in ccmGDB	C

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Phenotypic Information for ECHS1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ECHS1
	Familial Cancer Database: ECHS1

* 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_FATTY_ACID_METABOLISM KEGG_TRYPTOPHAN_METABOLISM KEGG_BETA_ALANINE_METABOLISM KEGG_PROPANOATE_METABOLISM KEGG_BUTANOATE_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: ECHS1
	MedGen: ECHS1 (Human Medical Genetics with Condition)
	ClinVar: ECHS1
Phenotype	MGI: ECHS1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ECHS1

Mutations for ECHS1

* 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 ECHS1 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
CV337393	JUP	4	338	17	39767336	39767921	ECHS1	335	398	10	135176370	135176434
AW518107	ENOX1	63	86	13	43912369	43912392	ECHS1	75	310	10	135176248	135178227
H39530	ECHS1	2	82	10	135184127	135184208	ECHS1	79	468	10	135176320	135180474

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=14

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=30)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr10:135186806-135186806	p.V11A	14
chr10:135179506-135179506	p.A238E	2
chr10:135184209-135184209	p.V47V	2
chr10:135179586-135179586	p.K211K	2
chr10:135184099-135184099	p.A84V	2
chr10:135178224-135178224	p.E249*	1
chr10:135180499-135180499	p.?	1
chr10:135184102-135184102	p.G83E	1
chr10:135182453-135182453	p.P163L	1
chr10:135184121-135184121	p.E77K	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		1		2	1		2		2			1	1				4	1		4
# mutation		1		2	1		2		2			1	1				4	1		5
nonsynonymous SNV				1	1		2		2			1	1				2	1		3
synonymous SNV		1		1													2			2

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
chr10:135179506	p.A238E	2
chr10:135179550	p.G195S	1
chr10:135184121	p.E156E	1
chr10:135179586	p.Y153C	1
chr10:135184164	p.G140G	1
chr10:135180429	p.A138V	1
chr10:135184202	p.F108C	1
chr10:135182473	p.M103I	1
chr10:135184238	p.A84V	1
chr10:135182483	p.K282N	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 ECHS1 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 ECHS1

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


AP2S1,AURKAIP1,UQCC3,C14orf2,CHCHD1,CUEDC2,DPCD, ECHS1,EDF1,MGMT,MRPL43,MRPS34,MTG1,NDUFB8, PAOX,PARK7,PPP2R2D,RNF181,TUBGCP2,USMG5,ZNF511	ABHD15,ACAA2,ACACB,ACOT1,ACOT2,ACSL1,ACSS2, AQP7,BOK,CIDEC,DECR1,DGAT1,HOGA1,ECHS1, FGFRL1,LGALS12,MLXIPL,MARC1,MARC2,PECR,PNPLA2

ATP5D,ATPIF1,AURKAIP1,C14orf2,C1QBP,COX8A,ECHS1, EIF5A,GOT1,MCAT,MRPL16,NDUFB8,NDUFS3,NUDT8, PCCB,PPP2R2D,RNMTL1,SDHB,TXN2,UQCRC1,ZNF511	ACADS,ACSF2,SUGCT,CEBPA,COQ4,COX5A,DECR1, DOLPP1,ECHS1,ESRRA,ETFDH,GJB1,HADH,HDHD3, LPCAT3,MGST3,PITX2,RAB20,RPP25,SLC27A4,TACO1

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 ECHS1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB00123	enoyl CoA hydratase, short chain, 1, mitochondrial	approved; nutraceutical	L-Lysine

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Cross referenced IDs for ECHS1

* 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