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 HSD3B2
Basic gene info.Gene symbolHSD3B2
Gene namehydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2
SynonymsHSD3B|HSDB|SDR11E2
CytomapUCSC genome browser: 1p13.1
Genomic locationchr1 :119957742-119965662
Type of geneprotein-coding
RefGenesNM_000198.3,
NM_001166120.1,
Ensembl idENSG00000203859
Description3 beta-HSD type II3 beta-hydroxysteroid dehydrogenase type II, delta 5-delta 4-isomerase type II, 3 beta-HSD type II3 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type 23 beta-hydroxysteroid dehydrogenase/Delta 5-->4-isomerase type II3-beta
Modification date20141207
dbXrefs MIM : 613890
HGNC : HGNC
Ensembl : ENSG00000203859
HPRD : 01941
Vega : OTTHUMG00000012526
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HSD3B2
BioGPS: 3284
Gene Expression Atlas: ENSG00000203859
The Human Protein Atlas: ENSG00000203859
PathwayNCI Pathway Interaction Database: HSD3B2
KEGG: HSD3B2
REACTOME: HSD3B2
ConsensusPathDB
Pathway Commons: HSD3B2
MetabolismMetaCyc: HSD3B2
HUMANCyc: HSD3B2
RegulationEnsembl's Regulation: ENSG00000203859
miRBase: chr1 :119,957,742-119,965,662
TargetScan: NM_000198
cisRED: ENSG00000203859
ContextiHOP: HSD3B2
cancer metabolism search in PubMed: HSD3B2
UCL Cancer Institute: HSD3B2
Assigned class in ccmGDBC

Top
Phenotypic Information for HSD3B2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HSD3B2
Familial Cancer Database: HSD3B2
* 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: HSD3B2
MedGen: HSD3B2 (Human Medical Genetics with Condition)
ClinVar: HSD3B2
PhenotypeMGI: HSD3B2 (International Mouse Phenotyping Consortium)
PhenomicDB: HSD3B2

Mutations for HSD3B2
* 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 HSD3B2 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

Top
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.

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=3

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=42)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr1:119958096-119958096p.I18I2
chr1:119964650-119964650p.G176S2
chr1:119965140-119965140p.Y339S2
chr1:119962135-119962135p.I79M2
chr1:119965071-119965071p.R316H2
chr1:119962109-119962109p.A71T2
chr1:119958092-119958092p.R17K1
chr1:119964637-119964637p.W171*1
chr1:119965137-119965137p.A338V1
chr1:119962113-119962113p.C72F1

Top
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
# sample23 5  3 1  1252  122 8
# mutation33 5  3 1  1652  152 9
nonsynonymous SNV33 4  2    1531  81 5
synonymous SNV   1  1 1  121  71 4
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
chr1:119958096p.I18I,HSD3B23
chr1:119964589p.P155P,HSD3B22
chr1:119962178p.E94K,HSD3B22
chr1:119958051p.W3C,HSD3B21
chr1:119964814p.S95S,HSD3B21
chr1:119962127p.W230C,HSD3B21
chr1:119964949p.Q311R,HSD3B21
chr1:119964561p.V99V,HSD3B21
chr1:119965158p.R237K,HSD3B21
chr1:119964834p.S324N,HSD3B21

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 HSD3B2 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 HSD3B2

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

AADAC,C1orf141,FOXL2NB,MGARP,CELA2A,CYP11A1,CYP17A1,
CYP19A1,FSHR,HSD3B1,HSD3B2,INHA,INSL3,KLHL4,
LHCGR,MBOAT4,MRO,REG3G,STAR,TCF21,TREML5P
ADAM2,AFMID,ALOX15B,DHRS2,HIST1H2BG,HIST1H4H,HPGD,
HSD3B1,HSD3B2,IDI1,LST-3TM12,MPV17L,PNLIPRP3,PPEF1,
SERHL2,SERHL,SULT1C3,TARP,UGT2B10,UGT2B11,UGT2B28

BEST4,CA2,DRD5,DUSP21,ENPP6,GBA3,GUCA2B,
HSD3B2,MEP1B,MS4A12,OSTalpha,OTOP2,SCNN1B,SCNN1G,
SLC14A2,SLC17A8,SLC25A34,SLC37A2,TEX11,TMIGD1,UGT2B15
ALDH1L1,ARRDC4,ART1,LINC01565,C8orf74,CAPN11,CCT8L2,
ERBB4,FAM138D,HSD3B2,HTR3D,LOC339240,LRRC6,LRRIQ4,
MFAP3L,MS4A12,SBK2,SERPINA11,SOX14,TEX101,WNT5A
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 HSD3B2
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 2approved; nutraceuticalNADH
DB01108hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2approved; withdrawn; investigationalTrilostane


Top
Cross referenced IDs for HSD3B2
* 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