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 HADH

Basic gene info.	Gene symbol	HADH
	Gene name	hydroxyacyl-CoA dehydrogenase
	Synonyms	HAD\|HADH1\|HADHSC\|HCDH\|HHF4\|MSCHAD\|SCHAD
	Cytomap	UCSC genome browser: 4q22-q26
	Genomic location	chr4 :108910869-108956331
	Type of gene	protein-coding
	RefGenes	NM_001184705.2, NM_005327.4,
	Ensembl id	ENSG00000138796
	Description	L-3-hydroxyacyl-Coenzyme A dehydrogenase, short chainhydroxyacyl-coenzyme A dehydrogenase, mitochondrialmedium and short-chain L-3-hydroxyacyl-coenzyme A dehydrogenaseshort-chain 3-hydroxyacyl-CoA dehydrogenase
	Modification date	20141219
dbXrefs	MIM : 601609
	HGNC : HGNC
	Ensembl : ENSG00000138796
	Vega : OTTHUMG00000131810
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HADH
	BioGPS: 3033
	Gene Expression Atlas: ENSG00000138796
	The Human Protein Atlas: ENSG00000138796
Pathway	NCI Pathway Interaction Database: HADH
	KEGG: HADH
	REACTOME: HADH
	ConsensusPathDB
	Pathway Commons: HADH
Metabolism	MetaCyc: HADH
	HUMANCyc: HADH
Regulation	Ensembl's Regulation: ENSG00000138796
	miRBase: chr4 :108,910,869-108,956,331
	TargetScan: NM_001184705
	cisRED: ENSG00000138796
Context	iHOP: HADH
	cancer metabolism search in PubMed: HADH
	UCL Cancer Institute: HADH
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: HADH
	Familial Cancer Database: HADH

* 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_BUTANOATE_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

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

Mutations for HADH

* 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
pancreas	HADH	chr4	108920782	108920802		chr4	74966341	74966361

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 HADH 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
BQ314823	HADH	11	372	4	108944648	108955491	NCL	365	595	2	232321427	232322411
AF133424	TSPAN16	9	1048	19	11406824	11437672	HADH	1047	1841	4	108940694	108955648
BF348759	HADH	2	351	4	108944669	108955491	NCL	344	403	2	232322352	232322411
AW375766	HADH	8	290	4	108955685	108955967	ATP5B	285	399	12	57031962	57032076
CB164018	HADH	1	78	4	108911008	108911085	HADH	78	636	4	108935650	108949090
BM504479	HADH	8	438	4	108911077	108935744	MEIS1	438	573	2	66784099	66784234

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=13)	Stat. for Synonymous SNVs (# total SNVs=7)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr4:108954337-108954337	p.A239T	3
chr4:108948850-108948850	p.P215S	1
chr4:108935703-108935703	p.V126V	1
chr4:108948853-108948853	p.G216W	1
chr4:108911097-108911097	p.F3F	1
chr4:108940705-108940705	p.I143M	1
chr4:108948914-108948914	p.R236Q	1
chr4:108911132-108911132	p.S15L	1
chr4:108940716-108940716	p.N147S	1
chr4:108954336-108954336	p.D238D	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	3	4			1		1		1	3	1	1				2		3
# mutation	1	2	3	4			1		1		1	3	1	1				2		3
nonsynonymous SNV	1	2	2	2					1		1	2	1					1		1
synonymous SNV			1	2			1					1		1				1		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
chr4:108954337	p.A239T,HADH	2
chr4:108935703	p.V126V,HADH	2
chr4:108955465	p.N245N	1
chr4:108940820	p.D238D,HADH	1
chr4:108911132	p.S15L,HADH	1
chr4:108948850	p.E242K,HADH	1
chr4:108911144	p.S19L,HADH	1
chr4:108948853	p.V265V,HADH	1
chr4:108930962	p.E60D,HADH	1
chr4:108953508	p.A282T,HADH	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 HADH 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 HADH

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 HADH

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
DB00157	hydroxyacyl-CoA dehydrogenase	approved; nutraceutical	NADH
DB01907	hydroxyacyl-CoA dehydrogenase	experimental	Nicotinamide-Adenine-Dinucleotide
DB03059	hydroxyacyl-CoA dehydrogenase	experimental	Acetoacetyl-Coenzyme A
DB03612	hydroxyacyl-CoA dehydrogenase	experimental	3-Hydroxybutyryl-Coenzyme A
DB00123	hydroxyacyl-CoA dehydrogenase	approved; nutraceutical	L-Lysine

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Cross referenced IDs for HADH

* 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