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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for BDH1 |
Basic gene info. | Gene symbol | BDH1 |
Gene name | 3-hydroxybutyrate dehydrogenase, type 1 | |
Synonyms | BDH|SDR9C1 | |
Cytomap | UCSC genome browser: 3q29 | |
Genomic location | chr3 :197236653-197282858 | |
Type of gene | protein-coding | |
RefGenes | NM_004051.4, NM_203314.2,NM_203315.2, | |
Ensembl id | ENSG00000161267 | |
Description | (R)-3-hydroxybutyrate dehydrogenase3-hydroxybutyrate dehydrogenase (heart, mitochondrial)D-beta-hydroxybutyrate dehydrogenase, mitochondrialshort chain dehydrogenase/reductase family 9C, member 1 | |
Modification date | 20141207 | |
dbXrefs | MIM : 603063 | |
HGNC : HGNC | ||
Ensembl : ENSG00000161267 | ||
HPRD : 04344 | ||
Vega : OTTHUMG00000155478 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_BDH1 | |
BioGPS: 622 | ||
Gene Expression Atlas: ENSG00000161267 | ||
The Human Protein Atlas: ENSG00000161267 | ||
Pathway | NCI Pathway Interaction Database: BDH1 | |
KEGG: BDH1 | ||
REACTOME: BDH1 | ||
ConsensusPathDB | ||
Pathway Commons: BDH1 | ||
Metabolism | MetaCyc: BDH1 | |
HUMANCyc: BDH1 | ||
Regulation | Ensembl's Regulation: ENSG00000161267 | |
miRBase: chr3 :197,236,653-197,282,858 | ||
TargetScan: NM_004051 | ||
cisRED: ENSG00000161267 | ||
Context | iHOP: BDH1 | |
cancer metabolism search in PubMed: BDH1 | ||
UCL Cancer Institute: BDH1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for BDH1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: BDH1 |
Familial Cancer Database: BDH1 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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_BUTANOATE_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: BDH1 |
MedGen: BDH1 (Human Medical Genetics with Condition) | |
ClinVar: BDH1 | |
Phenotype | MGI: BDH1 (International Mouse Phenotyping Consortium) |
PhenomicDB: BDH1 |
Mutations for BDH1 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows BDH1 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 |
BF679324 | BDH1 | 3 | 92 | 3 | 197249510 | 197249600 | UBR3 | 90 | 215 | 2 | 170938234 | 170938360 |
Other DBs for Structural Variants |
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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 | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   |   |   | 2 |   | 1 |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   | 2 |   | 1 |   |   |   |   |   |   | |||
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 |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=23) | (# total SNVs=8) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr3:197249622-197249622 | p.D100N | 2 |
chr3:197259282-197259282 | p.? | 2 |
chr3:197239189-197239189 | p.P203P | 2 |
chr3:197238877-197238877 | p.T307T | 2 |
chr3:197241203-197241203 | p.A165V | 1 |
chr3:197238892-197238892 | p.V302V | 1 |
chr3:197273237-197273237 | p.G26G | 1 |
chr3:197239128-197239128 | p.Y224H | 1 |
chr3:197241228-197241228 | p.S157G | 1 |
chr3:197238900-197238900 | p.D300N | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 | 1 |   | 4 | 1 |   | 2 |   | 1 |   |   | 3 | 6 | 1 |   |   | 5 | 6 | 1 | 3 |
# mutation | 1 | 1 |   | 4 | 1 |   | 2 |   | 1 |   |   | 3 | 6 | 1 |   |   | 5 | 6 | 1 | 3 |
nonsynonymous SNV |   | 1 |   | 3 |   |   | 1 |   | 1 |   |   | 2 | 5 | 1 |   |   | 3 | 4 | 1 | 2 |
synonymous SNV | 1 |   |   | 1 | 1 |   | 1 |   |   |   |   | 1 | 1 |   |   |   | 2 | 2 |   | 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 |
chr3:197238877 | p.T307T,BDH1 | 2 |
chr3:197239184 | p.A282T,BDH1 | 1 |
chr3:197260416 | p.S70L,BDH1 | 1 |
chr3:197238927 | p.D278N,BDH1 | 1 |
chr3:197241135 | p.G68W,BDH1 | 1 |
chr3:197273237 | p.G273C,BDH1 | 1 |
chr3:197238941 | p.P40S,BDH1 | 1 |
chr3:197241142 | p.V267V,BDH1 | 1 |
chr3:197273238 | p.G34C,BDH1 | 1 |
chr3:197238954 | p.P228H,BDH1 | 1 |
Other DBs for Point Mutations |
Copy Number for BDH1 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 BDH1 |
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. |
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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 |
ABCF3,ACAA1,ACY1,APOA1BP,BCAT2,BDH1,SYNE4, EIF2B5,FAAH,GCDH,MAGIX,NAPA,NECAB3,NMRAL1, NPRL2,PRDX2,RABEP2,SLC25A11,SPDEF,TCEA3,TXNRD2 | ACAD8,ACY1,APEH,BCAT2,BDH1,CPT2,DCXR, DOLPP1,ECHDC2,EEF2,GCAT,GGCT,GSTZ1,CLUH, MMAB,MRPS25,NUDT16L1,OPLAH,PPP1R16A,PRMT7,SLC25A38 | ||||
ACADS,BDH1,C6orf136,CC2D1A,CES3,DEGS2,ECHS1, FAAH,FAM162A,FUCA1,GGT6,LDHD,MCCC1,NDUFV1, NOXA1,PFKL,RPS6KA1,SUCLG2,TJP3,TMEM54,UQCRC1 | ADH1C,AGFG2,AP1M2,ASAP3,BDH1,CHCHD10,COX5A, CPT2,GJB1,GJB2,GSS,LDLRAP1,LGALS4,NDUFA10, NDUFS2,NDUFV1,PGM1,PPFIA3,RPP25,TRAF3IP2,TST |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for BDH1 |
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-hydroxybutyrate dehydrogenase, type 1 | approved; nutraceutical | NADH |
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Cross referenced IDs for BDH1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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