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 BDH2
Basic gene info.Gene symbolBDH2
Gene name3-hydroxybutyrate dehydrogenase, type 2
SynonymsDHRS6|EFA6R|PRO20933|SDR15C1|UCPA-OR|UNQ6308
CytomapUCSC genome browser: 4q24
Genomic locationchr4 :103998781-104021024
Type of geneprotein-coding
RefGenesNM_020139.3,
Ensembl idENSG00000164039
Description3-hydroxybutyrate dehydrogenase type 2R-beta-hydroxybutyrate dehydrogenasedehydrogenase/reductase (SDR family) member 6dehydrogenase/reductase SDR family member 6oxidoreductase UCPAshort chain dehydrogenase/reductase family 15C, member 1
Modification date20141207
dbXrefs HGNC : HGNC
HPRD : 07103
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_BDH2
BioGPS: 56898
Gene Expression Atlas: ENSG00000164039
The Human Protein Atlas: ENSG00000164039
PathwayNCI Pathway Interaction Database: BDH2
KEGG: BDH2
REACTOME: BDH2
ConsensusPathDB
Pathway Commons: BDH2
MetabolismMetaCyc: BDH2
HUMANCyc: BDH2
RegulationEnsembl's Regulation: ENSG00000164039
miRBase: chr4 :103,998,781-104,021,024
TargetScan: NM_020139
cisRED: ENSG00000164039
ContextiHOP: BDH2
cancer metabolism search in PubMed: BDH2
UCL Cancer Institute: BDH2
Assigned class in ccmGDBC

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Phenotypic Information for BDH2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: BDH2
Familial Cancer Database: BDH2
* 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_BUTANOATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: BDH2
MedGen: BDH2 (Human Medical Genetics with Condition)
ClinVar: BDH2
PhenotypeMGI: BDH2 (International Mouse Phenotyping Consortium)
PhenomicDB: BDH2

Mutations for BDH2
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows BDH2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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
There's no copy number variation information in COSMIC data for this gene.

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=21)
Stat. for Synonymous SNVs
(# total SNVs=3)
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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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
chr4:104016381-104016381p.Q44E2
chr4:104007675-104007675p.N127S2
chr4:104017366-104017366p.Q16E2
chr4:104013813-104013813p.Q64H2
chr4:104003289-104003289p.F211F2
chr4:104003299-104003299p.T208M2
chr4:104003301-104003301p.K207N1
chr4:104016360-104016360p.G51C1
chr4:104004068-104004068p.S184Y1
chr4:104016374-104016374p.L46P1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  3  2 2  1    11 4
# mutation2  3  2 2  1    11 4
nonsynonymous SNV2  1  1 1  1       4
synonymous SNV   2  1 1       11  
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
chr4:104003289p.F211F2
chr4:104004068p.L91L1
chr4:104004086p.L57F1
chr4:104012391p.G30V1
chr4:104012420p.R28S1
chr4:104000886p.G19G1
chr4:104013836p.L4F1
chr4:104000908p.V237V1
chr4:104016422p.A230D1
chr4:104003252p.L224V1

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 BDH2 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 BDH2

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

AASS,ABCD4,ALPK1,BDH2,BEND5,MSANTD2,C14orf93,
ADPRM,SPATA6L,DFNB59,GABARAP,LARP7,LOC286367,KAT8,
PHYHD1,PLEKHA4,RPL34,THYN1,TMEM91,TNFSF12,ZNF69
ANKRD49,ASB3,ASTE1,BDH2,TDRP,COMMD2,DYNC2LI1,
EFCAB7,FANCL,LRRC49,MITD1,N4BP2L1,PACRGL,POC5,
SRSF8,SLC35A1,TRAM1L1,ZDHHC13,ZDHHC6,ZNF140,ZNF20

BDH2,BDNF-AS,C11orf74,TBC1D32,CCDC122,FMO4,IYD,
LOC375190,LAMTOR3,MED4,NUDT7,PHYH,RSU1,RWDD3,
SEMA5A,SH3BGRL,TP53TG1,VAV3,ZC4H2,ZNF19,ZNF720
HYKK,AIG1,APOM,BDH2,BPHL,ADIRF,TMEM256,
CYB5A,DEGS2,DHRS7,GATA5,GATM,GOLT1A,GPX4,
HACL1,LOC201651,LRRC28,NR1H4,PEBP1,RNF141,TIGD2
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 BDH2


There's no related Drug.
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Cross referenced IDs for BDH2
* 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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