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 HSD3B1
Basic gene info.Gene symbolHSD3B1
Gene namehydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1
Synonyms3BETAHSD|HSD3B|HSDB3|HSDB3A|I|SDR11E1
CytomapUCSC genome browser: 1p13.1
Genomic locationchr1 :120049825-120057681
Type of geneprotein-coding
RefGenesNM_000862.2,
Ensembl idENSG00000203857
Description3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 13 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type I3-beta-HSD I3-beta-hydroxy-5-ene steroid dehydrogenase3-beta-hydroxy-Delta(5)-steroid dehydrogenasedelta-5-3-ketosteroid i
Modification date20141207
dbXrefs MIM : 109715
HGNC : HGNC
Ensembl : ENSG00000203857
HPRD : 04920
Vega : OTTHUMG00000012525
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HSD3B1
BioGPS: 3283
Gene Expression Atlas: ENSG00000203857
The Human Protein Atlas: ENSG00000203857
PathwayNCI Pathway Interaction Database: HSD3B1
KEGG: HSD3B1
REACTOME: HSD3B1
ConsensusPathDB
Pathway Commons: HSD3B1
MetabolismMetaCyc: HSD3B1
HUMANCyc: HSD3B1
RegulationEnsembl's Regulation: ENSG00000203857
miRBase: chr1 :120,049,825-120,057,681
TargetScan: NM_000862
cisRED: ENSG00000203857
ContextiHOP: HSD3B1
cancer metabolism search in PubMed: HSD3B1
UCL Cancer Institute: HSD3B1
Assigned class in ccmGDBC

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Phenotypic Information for HSD3B1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HSD3B1
Familial Cancer Database: HSD3B1
* 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_STEROID_HORMONES_AND_VITAMINS_A_AND_D
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HSD3B1
MedGen: HSD3B1 (Human Medical Genetics with Condition)
ClinVar: HSD3B1
PhenotypeMGI: HSD3B1 (International Mouse Phenotyping Consortium)
PhenomicDB: HSD3B1

Mutations for HSD3B1
* 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
skinHSD3B1chr1120050068120050068chr1120077813120077813
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 HSD3B1 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
GAIN (# sample)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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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=37)
Stat. for Synonymous SNVs
(# total SNVs=23)
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
chr1:120057158-120057158p.L338L3
chr1:120050152-120050152p.R18K2
chr1:120057246-120057246p.T367N2
chr1:120056674-120056674p.N176N2
chr1:120057081-120057081p.R312Q2
chr1:120050105-120050105p.T2T2
chr1:120056726-120056726p.G194R1
chr1:120057191-120057191p.A349S1
chr1:120050221-120050221p.P41L1
chr1:120054205-120054205p.D75D1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample11 101 1 1 1853  123 7
# mutation11 91 1 1 11263  133 8
nonsynonymous SNV11 5  1 1 1852  81 3
synonymous SNV   41      411  52 5
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
chr1:120056981p.A339V2
chr1:120056793p.G216E2
chr1:120056657p.G40R2
chr1:120057162p.G171W2
chr1:120050217p.R279C2
chr1:120056674p.N176N2
chr1:120056677p.G177G1
chr1:120050126p.Y292H1
chr1:120056930p.T9T1
chr1:120050223p.N52K1

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 HSD3B1 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 HSD3B1

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

AADAC,C1orf141,FOXL2NB,MGARP,CELA2A,CYP11A1,CYP17A1,
CYP19A1,FSHR,HSD11B1,HSD3B1,INHA,INSL3,KLHL4,
LHCGR,MBOAT4,MRO,REG3G,STAR,TCF21,TREML5P
ADAM2,AFMID,ALOX15B,AWAT2,B3GAT1,C6orf223,DHRS2,
HIST1H4H,HPGD,HSD3B1,HSD3B2,MPV17L,PNLIPRP3,PPEF1,
MSMO1,SERHL2,SLC5A11,SRD5A1,TARP,UGT2B10,UGT2B28

ABHD13,NCMAP,CCDC170,CRYL1,DIS3,DNAJC3,DPEP1,
ELSPBP1,EMX2,EMX2OS,GRTP1,HSD3B1,LAMP1,LIG4,
NDFIP2,SLC13A3,TM9SF2,TMEM211,TSC22D1,UBAC2,USP6NL
ABCG8,ALDOB,ERICH4,CRISP2,CYP2D6,CYP3A4,DHDH,
GSTA2,HAPLN4,HSD3B1,MGAM,NAT8,NTS,PDZK1P1,
RBP2,SHBG,SLC10A2,SLC13A1,SLC5A12,SLC6A4,TREH
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 HSD3B1
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
DB00157hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1approved; nutraceuticalNADH
DB01108hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1approved; withdrawn; investigationalTrilostane
DB01536hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1illicit; experimental4-Androstenedione


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Cross referenced IDs for HSD3B1
* 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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