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 HADHB

Basic gene info.	Gene symbol	HADHB
	Gene name	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit
	Synonyms	ECHB\|MTPB\|TP-BETA
	Cytomap	UCSC genome browser: 2p23
	Genomic location	chr2 :26467615-26513333
	Type of gene	protein-coding
	RefGenes	NM_000183.2, NM_001281512.1,NM_001281513.1,
	Ensembl id	ENSG00000138029
	Description	2-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 date	20141207
dbXrefs	MIM : 143450
	HGNC : HGNC
	Ensembl : ENSG00000138029
	HPRD : 00887
	Vega : OTTHUMG00000096978
Protein	UniProt: P55084 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HADHB
	BioGPS: 3032
	Gene Expression Atlas: ENSG00000138029
	The Human Protein Atlas: ENSG00000138029
Pathway	NCI Pathway Interaction Database: HADHB
	KEGG: HADHB
	REACTOME: HADHB
	ConsensusPathDB
	Pathway Commons: HADHB
Metabolism	MetaCyc: HADHB
	HUMANCyc: HADHB
Regulation	Ensembl's Regulation: ENSG00000138029
	miRBase: chr2 :26,467,615-26,513,333
	TargetScan: NM_000183
	cisRED: ENSG00000138029
Context	iHOP: HADHB
	cancer metabolism search in PubMed: HADHB
	UCL Cancer Institute: HADHB
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of HADHB in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_FATTY_ACID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	143450; gene. 609015; phenotype.
Orphanet	746; Mitochondrial trifunctional protein deficiency.
Disease	KEGG Disease: HADHB
	MedGen: HADHB (Human Medical Genetics with Condition)
	ClinVar: HADHB
Phenotype	MGI: HADHB (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	HADHB	chr2	26499144	26499144	GPR113	chr2	26541553	26541553
breast	HADHB	chr2	26500776	26500776		chr2	222957214	222957214
breast	HADHB	chr2	26500921	26500921	EFR3B	chr2	25373697	25373697
breast	HADHB	chr2	26500921	26500921	LY86-AS1	chr6	6402870	6402870
ovary	HADHB	chr2	26473261	26473281		chr2	38659886	38659906
ovary	HADHB	chr2	26492282	26492302	P2RY6	chr11	72996068	72996088

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 HADHB 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
DA426922	BOLA2	1	214	16	29830861	29831656	HADHB	212	522	2	26486245	26499999
AI004639	HADHB	2	100	2	26512870	26512968	AHSA1	95	253	14	77928517	77929074

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=3

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Somatic 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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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
chr2:26501519-26501519	p.I160I	3
chr2:26502875-26502875	p.V275V	3
chr2:26501646-26501646	p.R203*	3
chr2:26508429-26508429	p.A460V	2
chr2:26486347-26486347	p.S70L	2
chr2:26492866-26492866	p.?	2
chr2:26501647-26501647	p.R203Q	2
chr2:26507820-26507820	p.T407A	1
chr2:26486264-26486264	p.T42T	1
chr2:26501657-26501657	p.F206F	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=3

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	2		9			2		3			5	4	1		1	6	4		7
# mutation	2	2		9			2		3			5	4	1		1	6	4		7
nonsynonymous SNV	2	2		8			1		3			5	3			1	2	4		4
synonymous SNV				1			1						1	1			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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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
chr2:26501519	p.I145I,HADHB	3
chr2:26501647	p.R188Q,HADHB	2
chr2:26486289	p.I51L,HADHB	2
chr2:26502035	p.L65L,HADHB	1
chr2:26486322	p.F187F,HADHB	1
chr2:26502980	p.A320T,HADHB	1
chr2:26501535	p.S70L,HADHB	1
chr2:26502041	p.Q335H,HADHB	1
chr2:26486333	p.P76T,HADHB	1
chr2:26505782	p.F191F,HADHB	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 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

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


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

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 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