Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 HADHB
Basic gene info.Gene symbolHADHB
Gene namehydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit
SynonymsECHB|MTPB|TP-BETA
CytomapUCSC genome browser: 2p23
Genomic locationchr2 :26467615-26513333
Type of geneprotein-coding
RefGenesNM_000183.2,
NM_001281512.1,NM_001281513.1,
Ensembl idENSG00000138029
Description2-enoyl-Coenzyme A (CoA) hydratase, beta subunit3-ketoacyl-Coenzyme A (CoA) thiolase of mitochondrial trifunctional protein, beta subunitacetyl-CoA acyltransferasebeta-ketothiolasehydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/eno
Modification date20141207
dbXrefs MIM : 143450
HGNC : HGNC
Ensembl : ENSG00000138029
HPRD : 00887
Vega : OTTHUMG00000096978
ProteinUniProt: P55084
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HADHB
BioGPS: 3032
Gene Expression Atlas: ENSG00000138029
The Human Protein Atlas: ENSG00000138029
PathwayNCI Pathway Interaction Database: HADHB
KEGG: HADHB
REACTOME: HADHB
ConsensusPathDB
Pathway Commons: HADHB
MetabolismMetaCyc: HADHB
HUMANCyc: HADHB
RegulationEnsembl's Regulation: ENSG00000138029
miRBase: chr2 :26,467,615-26,513,333
TargetScan: NM_000183
cisRED: ENSG00000138029
ContextiHOP: HADHB
cancer metabolism search in PubMed: HADHB
UCL Cancer Institute: HADHB
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of HADHB in cancer cell metabolism1. Mazzio EA, Boukli N, Rivera N, Soliman KF (2012) Pericellular pH homeostasis is a primary function of the Warburg effect: inversion of metabolic systems to control lactate steady state in tumor cells. Cancer Sci 103: 422-432. doi: 10.1111/j.1349-7006.2012.02206.x. pmid: 3294166. go to article
2. Zhou Z, Zhou J, Du Y (2012) Estrogen receptor alpha interacts with mitochondrial protein HADHB and affects beta-oxidation activity. Mol Cell Proteomics 11: M111 011056. doi: 10.1074/mcp.M111.011056. pmid: 3394935. go to article
3. Fernandez-Hernando C, Suarez Y, Rayner KJ, Moore KJ (2011) MicroRNAs in lipid metabolism. Curr Opin Lipidol 22: 86-92. doi: 10.1097/MOL.0b013e3283428d9d. pmid: 3096067. go to article
4. Zhou Z, Zhou J, Du Y (2012) Estrogen receptor beta interacts and colocalizes with HADHB in mitochondria. Biochem Biophys Res Commun 427: 305-308. doi: 10.1016/j.bbrc.2012.09.047. pmid: 3485071. go to article

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Phenotypic Information for HADHB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HADHB
Familial Cancer Database: HADHB
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 143450; gene.
609015; phenotype.
Orphanet 746; Mitochondrial trifunctional protein deficiency.
DiseaseKEGG Disease: HADHB
MedGen: HADHB (Human Medical Genetics with Condition)
ClinVar: HADHB
PhenotypeMGI: HADHB (International Mouse Phenotyping Consortium)
PhenomicDB: HADHB

Mutations for HADHB
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastHADHBchr22649914426499144GPR113chr22654155326541553
breastHADHBchr22650077626500776chr2222957214222957214
breastHADHBchr22650092126500921EFR3Bchr22537369725373697
breastHADHBchr22650092126500921LY86-AS1chr664028706402870
ovaryHADHBchr22647326126473281chr23865988638659906
ovaryHADHBchr22649228226492302P2RY6chr117299606872996088
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HADHB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA426922BOLA21214162983086129831656HADHB21252222648624526499999
AI004639HADHB210022651287026512968AHSA195253147792851777929074

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

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1       1 1      
GAIN (# sample)1                
LOSS (# sample)        1 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)

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=36)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr2:26501646-26501646p.R203*3
chr2:26501519-26501519p.I160I3
chr2:26502875-26502875p.V275V3
chr2:26492866-26492866p.?2
chr2:26501647-26501647p.R203Q2
chr2:26508429-26508429p.A460V2
chr2:26486347-26486347p.S70L2
chr2:26499942-26499942p.A119V1
chr2:26505766-26505766p.M329I1
chr2:26477130-26477131p.I3_L4insY1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 9  2 3  541 164 7
# mutation22 9  2 3  541 164 7
nonsynonymous SNV22 8  1 3  53  124 4
synonymous SNV   1  1     11  4  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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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
chr2:26501519p.I145I,HADHB3
chr2:26501647p.I51L,HADHB2
chr2:26486289p.R188Q,HADHB2
chr2:26501645p.R20I,HADHB1
chr2:26477181p.L152L,HADHB1
chr2:26502894p.R267C,HADHB1
chr2:26496570p.T42T,HADHB1
chr2:26486264p.S154P,HADHB1
chr2:26502916p.M274T,HADHB1
chr2:26496613p.D170H,HADHB1

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 HADHB 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 HADHB

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))
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check002.gifCNV 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
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

BRE,SLC35F6,DYNC2LI1,GTF3C2,HADHA,HADHB,IMMT,
LAPTM4A,MRPL19,MRPL35,NDUFA10,PCCB,PRDX3,PREPL,
RAB10,RBKS,SH3YL1,SRBD1,TRMT61B,UQCRC2,YPEL5
ACAT1,ATP5B,ADCK3,COX5A,EPM2A,MTFR1L,FH,
HADHB,KLHL31,NDUFS1,NNT,NRD1,PDHX,PHYH,
PPP3CB,RRAGD,RXRG,SCN4A,SDHB,SNTA1,UQCRFS1

ACADS,ATP5A1,ATP5G3,CES3,CPT2,ECHS1,FASTKD1,
HADHA,HADHB,IMMT,KIAA0391,MDH1,MRPL35,AP5M1,
NAT1,NDUFA10,PCCB,SDHD,SUCLG1,UQCRC1,UQCRC2
ACSL5,AKR1B10,BTD,CROT,CYP2B6,CYP2C18,GDPD2,
HADHA,HADHB,HSD17B11,NCOA4,PBLD,PGRMC1,PRAP1,
RBKS,SLC23A3,SLC3A1,SNX24,TMBIM6,TMEM82,TOR1AIP2
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

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check002.gifInteracting 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 HADHB


There's no related Drug.
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Cross referenced IDs for HADHB
* 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



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