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 HSD17B1
Basic gene info.Gene symbolHSD17B1
Gene namehydroxysteroid (17-beta) dehydrogenase 1
SynonymsEDH17B2|EDHB17|HSD17|SDR28C1
CytomapUCSC genome browser: 17q11-q21
Genomic locationchr17 :40703983-40707232
Type of geneprotein-coding
RefGenesNM_000413.2,
Ensembl idENSG00000108786
Description17-beta-HSD 117-beta-hydroxysteroid dehydrogenase type 120 alpha-hydroxysteroid dehydrogenase20-alpha-HSDE2DHestradiol 17-beta-dehydrogenase 1estradiol 17-beta-dehydrogenase-1hydroxysteroid (17-beta) dehydrogenase 1 isoformplacental 17-beta-hydrox
Modification date20141207
dbXrefs MIM : 109684
HGNC : HGNC
HPRD : 00185
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HSD17B1
BioGPS: 3292
Gene Expression Atlas: ENSG00000108786
The Human Protein Atlas: ENSG00000108786
PathwayNCI Pathway Interaction Database: HSD17B1
KEGG: HSD17B1
REACTOME: HSD17B1
ConsensusPathDB
Pathway Commons: HSD17B1
MetabolismMetaCyc: HSD17B1
HUMANCyc: HSD17B1
RegulationEnsembl's Regulation: ENSG00000108786
miRBase: chr17 :40,703,983-40,707,232
TargetScan: NM_000413
cisRED: ENSG00000108786
ContextiHOP: HSD17B1
cancer metabolism search in PubMed: HSD17B1
UCL Cancer Institute: HSD17B1
Assigned class in ccmGDBC

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Phenotypic Information for HSD17B1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HSD17B1
Familial Cancer Database: HSD17B1
* 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: HSD17B1
MedGen: HSD17B1 (Human Medical Genetics with Condition)
ClinVar: HSD17B1
PhenotypeMGI: HSD17B1 (International Mouse Phenotyping Consortium)
PhenomicDB: HSD17B1

Mutations for HSD17B1
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 HSD17B1 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=14

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr17:40706906-40706906p.G313S14
chr17:40705294-40705294p.R84C2
chr17:40704977-40704977p.T9S1
chr17:40706777-40706777p.D270N1
chr17:40705464-40705464p.N91N1
chr17:40706435-40706435p.I184M1
chr17:40705030-40705030p.P27T1
chr17:40706825-40706825p.G286R1
chr17:40705487-40705495p.E101_L103delEAL1
chr17:40706441-40706441p.C186C1

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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  4  1 1 1 2   16 5
# mutation2  4  1 1 1 2   16 5
nonsynonymous SNV1  2    1 1 1    4 3
synonymous SNV1  2  1     1   12 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
chr17:40704977p.P57L1
chr17:40705591p.E202D1
chr17:40706825p.T62T1
chr17:40705214p.D206A1
chr17:40705593p.D66D1
chr17:40706846p.Q232R1
chr17:40705230p.V80V1
chr17:40705607p.E258E1
chr17:40705242p.R84C1
chr17:40705828p.D270N1

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 HSD17B1 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 HSD17B1

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

ACTR2,API5,CHAC2,CMPK1,DLAT,FAM98A,HSD17B12,
LRRC8B,MRPL19,MTCH2,MTMR2,NUP160,NUS1,PPP1CB,
PPP3R1,DESI2,RAB1A,RRAS2,TMEM123,UGP2,ZFAND5
ALG9,AZI2,BNIP3L,SMIM3,CCDC50,CCNH,CEPT1,
RHOV___CHP1,CRLS1,CTNNAL1,ECHDC1,FBXL5,GPR180,HSD17B12,
LYRM1,OSBPL1A,PPP2R5A,PPP3R1,RTN3,STK39,TMEM135

ACAT2,CCNC,CMC1,COX11,EIF3M,HSD17B12,HSD17B7,
IDI1,IMMP1L,MRPL1,MRPL42,MRPL48,MTCH2,PSMA1,
RSL24D1,MSMO1,SC5D,SRSF3,SRP9,TMEM135,UBE2N
ADH1C,ALG2,ASAP3,CAAP1,DNASE2B,DTWD2,FAM81A,
GRSF1,HPGDS,HSD17B12,IGFBP2,ITGB6,KCNV1,MEST,
AP5M1,NARS,PREP,PROM2,PTGER2,SLC4A10,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

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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 HSD17B1
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 1approved; nutraceuticalNADH
DB01536hydroxysteroid (17-beta) dehydrogenase 1illicit; experimental4-Androstenedione
DB01561hydroxysteroid (17-beta) dehydrogenase 1illicit; experimentalAndrostanedione
DB01708hydroxysteroid (17-beta) dehydrogenase 1nutraceuticalDehydroepiandrosterone
DB01907hydroxysteroid (17-beta) dehydrogenase 1experimentalNicotinamide-Adenine-Dinucleotide
DB02187hydroxysteroid (17-beta) dehydrogenase 1experimentalEquilin
DB02323hydroxysteroid (17-beta) dehydrogenase 1experimentalEM-1745
DB02901hydroxysteroid (17-beta) dehydrogenase 1illicit; experimentalDihydrotestosterone
DB03461hydroxysteroid (17-beta) dehydrogenase 1experimental2'-Monophosphoadenosine 5'-Diphosphoribose


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Cross referenced IDs for HSD17B1
* 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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