Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolECHS1
Gene nameenoyl CoA hydratase, short chain, 1, mitochondrial
SynonymsSCEH
CytomapUCSC genome browser: 10q26.2-q26.3
Genomic locationchr10 :135175986-135186908
Type of geneprotein-coding
RefGenesNM_004092.3,
Ensembl idENSG00000127884
Descriptionenoyl Coenzyme A hydratase, short chain, 1, mitochondrialenoyl-CoA hydratase 1enoyl-CoA hydratase, mitochondrialshort-chain enoyl-CoA hydratase
Modification date20141207
dbXrefs MIM : 602292
HGNC : HGNC
Ensembl : ENSG00000127884
HPRD : 03799
Vega : OTTHUMG00000019320
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ECHS1
BioGPS: 1892
Gene Expression Atlas: ENSG00000127884
The Human Protein Atlas: ENSG00000127884
PathwayNCI Pathway Interaction Database: ECHS1
KEGG: ECHS1
REACTOME: ECHS1
ConsensusPathDB
Pathway Commons: ECHS1
MetabolismMetaCyc: ECHS1
HUMANCyc: ECHS1
RegulationEnsembl's Regulation: ENSG00000127884
miRBase: chr10 :135,175,986-135,186,908
TargetScan: NM_004092
cisRED: ENSG00000127884
ContextiHOP: ECHS1
cancer metabolism search in PubMed: ECHS1
UCL Cancer Institute: ECHS1
Assigned class in ccmGDBC

Top
Phenotypic Information for ECHS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ECHS1
MedGen: ECHS1 (Human Medical Genetics with Condition)
ClinVar: ECHS1
PhenotypeMGI: ECHS1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ECHS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CV337393JUP4338173976733639767921ECHS133539810135176370135176434
AW518107ENOX16386134391236943912392ECHS17531010135176248135178227
H39530ECHS128210135184127135184208ECHS17946810135176320135180474

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample11               
GAIN (# sample)1                
LOSS (# sample) 1               
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)

Top
check002.gifSNV 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

Top
check002.gifSomatic 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.

Top
check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr10:135186806-135186806p.V11A14
chr10:135184209-135184209p.V47V2
chr10:135179586-135179586p.K211K2
chr10:135184099-135184099p.A84V2
chr10:135179506-135179506p.A238E2
chr10:135182473-135182473p.E156E1
chr10:135184202-135184202p.I50F1
chr10:135179547-135179547p.Q224H1
chr10:135182515-135182515p.G142G1
chr10:135176384-135176384p.F287L1

Top
check002.gifSNV 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 ID1234567891011121314151617181920
# sample 1 21 2 2  11   41 4
# mutation 1 21 2 2  11   41 5
nonsynonymous SNV   11 2 2  11   21 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])

Top
check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr10:135179506p.A238E2
chr10:135184238p.M103I1
chr10:135182483p.A84V1
chr10:135176399p.K282N1
chr10:135182521p.G83V1
chr10:135176413p.A278T1
chr10:135183409p.E77K1
chr10:135176419p.M276V1
chr10:135183499p.C62C1
chr10:135178183p.L262L1

check002.gifOther 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

check002.gifCopy 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]

Top
Gene Expression for ECHS1

check002.gifGene 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.

check002.gifDifferential 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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
Gene-Gene Network Information
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for ECHS1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00123enoyl CoA hydratase, short chain, 1, mitochondrialapproved; nutraceuticalL-Lysine


Top
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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas