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 HSD17B3
Basic gene info.Gene symbolHSD17B3
Gene namehydroxysteroid (17-beta) dehydrogenase 3
SynonymsEDH17B3|SDR12C2
CytomapUCSC genome browser: 9q22
Genomic locationchr9 :98997588-99064434
Type of geneprotein-coding
RefGenesNM_000197.1,
Ensembl idENSG00000130948
Description17-beta-HSD 317-beta-HSD317-beta-hydroxysteroid dehydrogenase type 3short chain dehydrogenase/reductase family 12C, member 2testicular 17-beta-hydroxysteroid dehydrogenasetestosterone 17-beta-dehydrogenase 3
Modification date20141207
dbXrefs MIM : 605573
HGNC : HGNC
Ensembl : ENSG00000130948
HPRD : 05716
Vega : OTTHUMG00000020292
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HSD17B3
BioGPS: 3293
Gene Expression Atlas: ENSG00000130948
The Human Protein Atlas: ENSG00000130948
PathwayNCI Pathway Interaction Database: HSD17B3
KEGG: HSD17B3
REACTOME: HSD17B3
ConsensusPathDB
Pathway Commons: HSD17B3
MetabolismMetaCyc: HSD17B3
HUMANCyc: HSD17B3
RegulationEnsembl's Regulation: ENSG00000130948
miRBase: chr9 :98,997,588-99,064,434
TargetScan: NM_000197
cisRED: ENSG00000130948
ContextiHOP: HSD17B3
cancer metabolism search in PubMed: HSD17B3
UCL Cancer Institute: HSD17B3
Assigned class in ccmGDBC

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Phenotypic Information for HSD17B3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HSD17B3
Familial Cancer Database: HSD17B3
* 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: HSD17B3
MedGen: HSD17B3 (Human Medical Genetics with Condition)
ClinVar: HSD17B3
PhenotypeMGI: HSD17B3 (International Mouse Phenotyping Consortium)
PhenomicDB: HSD17B3

Mutations for HSD17B3
* 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
ovaryHSD17B3chr99904570299045722SLC35D2chr99910099699101016
ovaryHSD17B3chr99905928799059307chr99892620498926224
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 HSD17B3 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 # sample        1     1  
GAIN (# sample)        1     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=23)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr9:99007679-99007679p.S185F3
chr9:99007682-99007682p.S184Y3
chr9:99006664-99006664p.A207T2
chr9:99060718-99060718p.G61W2
chr9:99060732-99060732p.A56V2
chr9:99064321-99064321p.A22A2
chr9:98997817-98997817p.F286F2
chr9:99006625-99006625p.E220*2
chr9:99017173-99017173p.L85P1
chr9:98997839-98997839p.S279N1

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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
# sample11 11 1    5 1 181 6
# mutation11 11 1    5 1 181 6
nonsynonymous SNV1  11 1    3   151 4
synonymous SNV 1         2 1  3  2
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
chr9:98997839p.I150I1
chr9:99013703p.E149K1
chr9:99064321p.H142Y1
chr9:99003054p.P136S1
chr9:99013708p.F286L1
chr9:99064323p.E114K1
chr9:99003062p.A283D1
chr9:99013729p.S279N1
chr9:99064372p.T108R1
chr9:99003063p.A270T1

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 HSD17B3 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 HSD17B3

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

BNC1,C11orf87,CDH4,COL17A1,FGFBP1,HAS3,HMGA2,
HSD17B3,KRT5,KRT75,LOC150527,MT4,MYO7B,OR2J3,
PADI3,PCSK9,PLEK2,RPSAP52,S100A2,SOX15,TNFSF9
AMT,CATSPER2,CCNL2,DCST2,GNB3,HSD17B3,IFT27,
KIF12,LOC100128288,LOC390595,LOC440944,LUC7L,MYO15A,SEPT7P2,
SETD4,SLC23A3,TFAP2E,THOC1,TTLL9,WASH7P,ZNF789

AGBL2,C12orf42,MROH7,MLLT4-AS1,CCNL2,CROCCP3,DNHD1,
HGFAC,HSD17B3,KLHL31,LOC100270804,NPHP3,NTN5,PAK7,
SOHLH1,TCHH,TCTE3,TEX19,THSD1P1,ZNF735,ZNF83
TMEM74B,CCDC108,CREB3L3,CYP2C9,CYP4F2,CYP4F3,DGAT1,
DNASE1,FAM151A,FGF19,HAPLN4,HSD17B3,MLXIPL,MUC17,
PLB1,SI,SLC5A2,SULT1E1,UGT1A3,UGT1A4,UGT1A5
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 HSD17B3
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
DB00157hydroxysteroid (17-beta) dehydrogenase 3approved; nutraceuticalNADH
DB00396hydroxysteroid (17-beta) dehydrogenase 3approvedProgesterone
DB00624hydroxysteroid (17-beta) dehydrogenase 3approved; investigationalTestosterone


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Cross referenced IDs for HSD17B3
* 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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