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 HIBADH

Basic gene info.	Gene symbol	HIBADH
	Gene name	3-hydroxyisobutyrate dehydrogenase
	Synonyms	NS5ATP1
	Cytomap	UCSC genome browser: 7p15.2
	Genomic location	chr7 :27565058-27702620
	Type of gene	protein-coding
	RefGenes	NM_152740.3,
	Ensembl id	ENSG00000106049
	Description	3'-hydroxyisobutyrate dehydrogenase3-hydroxyisobutyrate dehydrogenase, mitochondrial
	Modification date	20141207
dbXrefs	MIM : 608475
	HGNC : HGNC
	Ensembl : ENSG00000106049
	HPRD : 12238
	Vega : OTTHUMG00000097035
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HIBADH
	BioGPS: 11112
	Gene Expression Atlas: ENSG00000106049
	The Human Protein Atlas: ENSG00000106049
Pathway	NCI Pathway Interaction Database: HIBADH
	KEGG: HIBADH
	REACTOME: HIBADH
	ConsensusPathDB
	Pathway Commons: HIBADH
Metabolism	MetaCyc: HIBADH
	HUMANCyc: HIBADH
Regulation	Ensembl's Regulation: ENSG00000106049
	miRBase: chr7 :27,565,058-27,702,620
	TargetScan: NM_152740
	cisRED: ENSG00000106049
Context	iHOP: HIBADH
	cancer metabolism search in PubMed: HIBADH
	UCL Cancer Institute: HIBADH
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: HIBADH
	Familial Cancer Database: HIBADH

* 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
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

Mutations for HIBADH

* 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
breast	HIBADH	chr7	27639557	27639557		chr7	32939144	32939144
ovary	HIBADH	chr7	27607711	27607731	HIBADH	chr7	27594367	27594387

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 HIBADH 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
BQ346350	HIBADH	14	142	7	27595618	27595747	MARCH6	130	217	5	10411628	10414610
BG003402	RBM19	6	136	12	114315455	114315587	HIBADH	117	439	7	27693438	27693762
BQ346303	HIBADH	14	142	7	27595618	27595747	MARCH6	130	217	5	10411628	10414610

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=19)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr7:27689145-27689145	p.I67V	2
chr7:27570874-27570874	p.V263V	2
chr7:27582704-27582704	p.R167Q	2
chr7:27669029-27669029	p.K149E	1
chr7:27565960-27565960	p.S295N	1
chr7:27578011-27578011	p.L215P	1
chr7:27669039-27669039	p.K145K	1
chr7:27689153-27689153	p.P64L	1
chr7:27565971-27565971	p.D291D	1
chr7:27582591-27582591	p.G205R	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		4			1		2				1	1		1	7	4	1	6
# mutation		1		4			1		2				1	1		1	8	4	1	6
nonsynonymous SNV		1		2			1		1				1				6	3		5
synonymous SNV				2					1					1		1	2	1	1	1

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
chr7:27672063	p.A138T	1
chr7:27565971	p.D291D	1
chr7:27582693	p.P137S	1
chr7:27689115	p.A270T	1
chr7:27570855	p.G126G	1
chr7:27582704	p.P268L	1
chr7:27689129	p.L120L	1
chr7:27570860	p.G266G	1
chr7:27669002	p.E94K	1
chr7:27689131	p.V263V	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 HIBADH 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 HIBADH

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


BBS9,MALSU1,C7orf31,CBX3,DKFZP586I1420,DPY19L1,SPATA31D4, SPATA31D5P,SPATA31D3,HIBADH,KBTBD2,KLHL7,LOC441204,LSM5, NT5C3A,NUPL2,PLEKHA8,RP9,RP9P,SCRN1,TAX1BP1	ADHFE1,ANKRD46,ATPAF1,BCL2L13,BNIP3,MROH8,CS, DECR1,DLD,ETFA,HIBADH,HSDL2,IARS2,IPO5, KIAA0408,NDUFB5,PFKFB1,RNF157,STRADB,SUCLA2,SUCLG2

BZW2,MPLKIP,C7orf25,MALSU1,FAM220A,CBX3,CCT6A, CRCP,EIF2AK1,GBAS,HIBADH,IMMP2L,MIOS,NUPL2, PSMA2,SUMF2,TBRG4,TWISTNB,UBE2D4,ZDHHC4,ZNRF2	ARL3,BEX4,AKIP1,C11orf74,C1orf123,FAM210B,CAMLG, CBY1,CRYZL1,DEPTOR,DUSP19,EID1,FAM172A,GNPAT, HIBADH,MSTN,NME7,RPL23AP82,RYK,TMEM123,ZNF639

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 HIBADH

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	3-hydroxyisobutyrate dehydrogenase	approved; nutraceutical	NADH
DB00161	3-hydroxyisobutyrate dehydrogenase	approved; nutraceutical	L-Valine

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Cross referenced IDs for HIBADH

* 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