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 HIBADH
Basic gene info.Gene symbolHIBADH
Gene name3-hydroxyisobutyrate dehydrogenase
SynonymsNS5ATP1
CytomapUCSC genome browser: 7p15.2
Genomic locationchr7 :27565058-27702620
Type of geneprotein-coding
RefGenesNM_152740.3,
Ensembl idENSG00000106049
Description3'-hydroxyisobutyrate dehydrogenase3-hydroxyisobutyrate dehydrogenase, mitochondrial
Modification date20141207
dbXrefs MIM : 608475
HGNC : HGNC
Ensembl : ENSG00000106049
HPRD : 12238
Vega : OTTHUMG00000097035
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HIBADH
BioGPS: 11112
Gene Expression Atlas: ENSG00000106049
The Human Protein Atlas: ENSG00000106049
PathwayNCI Pathway Interaction Database: HIBADH
KEGG: HIBADH
REACTOME: HIBADH
ConsensusPathDB
Pathway Commons: HIBADH
MetabolismMetaCyc: HIBADH
HUMANCyc: HIBADH
RegulationEnsembl's Regulation: ENSG00000106049
miRBase: chr7 :27,565,058-27,702,620
TargetScan: NM_152740
cisRED: ENSG00000106049
ContextiHOP: HIBADH
cancer metabolism search in PubMed: HIBADH
UCL Cancer Institute: HIBADH
Assigned class in ccmGDBC

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

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

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

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastHIBADHchr72763955727639557chr73293914432939144
ovaryHIBADHchr72760771127607731HIBADHchr72759436727594387
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 HIBADH related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ346350HIBADH1414272759561827595747MARCH613021751041162810414610
BG003402RBM19613612114315455114315587HIBADH11743972769343827693762
BQ346303HIBADH1414272759561827595747MARCH613021751041162810414610

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 # sample 2 1    4 1      
GAIN (# sample) 2 1    4        
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=2

Top
check002.gifSomatic 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.

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
chr7:27689145-27689145p.I67V2
chr7:27570874-27570874p.V263V2
chr7:27582704-27582704p.R167Q2
chr7:27669029-27669029p.K149E1
chr7:27565960-27565960p.S295N1
chr7:27578011-27578011p.L215P1
chr7:27669039-27669039p.K145K1
chr7:27689153-27689153p.P64L1
chr7:27565971-27565971p.D291D1
chr7:27582591-27582591p.G205R1

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 4  1 2   11 17416
# mutation 1 4  1 2   11 18416
nonsynonymous SNV 1 2  1 1   1   63 5
synonymous SNV   2    1    1 12111
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
chr7:27672063p.A138T1
chr7:27565971p.D291D1
chr7:27582693p.P137S1
chr7:27689115p.A270T1
chr7:27570855p.G126G1
chr7:27582704p.P268L1
chr7:27689129p.L120L1
chr7:27570860p.G266G1
chr7:27669002p.E94K1
chr7:27689131p.V263V1

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 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]

Top
Gene Expression for HIBADH

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

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
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 HIBADH
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
DB001573-hydroxyisobutyrate dehydrogenaseapproved; nutraceuticalNADH
DB001613-hydroxyisobutyrate dehydrogenaseapproved; nutraceuticalL-Valine


Top
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



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