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 HSD17B4
Basic gene info.Gene symbolHSD17B4
Gene namehydroxysteroid (17-beta) dehydrogenase 4
SynonymsDBP|MFE-2|MPF-2|PRLTS1|SDR8C1
CytomapUCSC genome browser: 5q21
Genomic locationchr5 :118788201-118878030
Type of geneprotein-coding
RefGenesNM_001199291.2,
NM_001292027.1,NM_001292028.1,NM_000414.3,NM_001199292.1,
Ensembl idENSG00000133835
Description17-beta-HSD 417-beta-HSD IV17-beta-hydroxysteroid dehydrogenase 417beta-estradiol dehydrogenase type IV3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydrataseD-3-hydroxyacyl-CoA dehydrataseD-bifunctional protein, peroxisomalbeta-h
Modification date20141207
dbXrefs MIM : 601860
HGNC : HGNC
Ensembl : ENSG00000133835
HPRD : 03514
Vega : OTTHUMG00000128899
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HSD17B4
BioGPS: 3295
Gene Expression Atlas: ENSG00000133835
The Human Protein Atlas: ENSG00000133835
PathwayNCI Pathway Interaction Database: HSD17B4
KEGG: HSD17B4
REACTOME: HSD17B4
ConsensusPathDB
Pathway Commons: HSD17B4
MetabolismMetaCyc: HSD17B4
HUMANCyc: HSD17B4
RegulationEnsembl's Regulation: ENSG00000133835
miRBase: chr5 :118,788,201-118,878,030
TargetScan: NM_001199291
cisRED: ENSG00000133835
ContextiHOP: HSD17B4
cancer metabolism search in PubMed: HSD17B4
UCL Cancer Institute: HSD17B4
Assigned class in ccmGDBC

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Phenotypic Information for HSD17B4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HSD17B4
Familial Cancer Database: HSD17B4
* 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_PEROXISOMAL_LIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HSD17B4
MedGen: HSD17B4 (Human Medical Genetics with Condition)
ClinVar: HSD17B4
PhenotypeMGI: HSD17B4 (International Mouse Phenotyping Consortium)
PhenomicDB: HSD17B4

Mutations for HSD17B4
* 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
ovaryHSD17B4chr5118805472118805492HSD17B4chr5118808041118808061
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 HSD17B4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF033554HSD17B414515118844842118865606COPS3444557171715020417150317

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=49)
Stat. for Synonymous SNVs
(# total SNVs=14)
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
chr5:118861713-118861713p.I559V3
chr5:118835235-118835235p.I399T2
chr5:118860945-118860945p.P513L2
chr5:118810095-118810095p.?2
chr5:118827800-118827800p.G240G2
chr5:118835117-118835117p.D360Y2
chr5:118814698-118814698p.Q202E2
chr5:118824886-118824886p.?2
chr5:118813124-118813124p.R121K2
chr5:118865666-118865666p.T615T2

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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
# sample2659  5 21 611 155 9
# mutation2659  5 21 611 155 10
nonsynonymous SNV2537  3 21 411 154 10
synonymous SNV 122  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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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
chr5:118835235p.R103K,HSD17B42
chr5:118813124p.I381T,HSD17B42
chr5:118865666p.A178G,HSD17B42
chr5:118814681p.T597T,HSD17B42
chr5:118872202p.K313E,HSD17B41
chr5:118835234p.R488H,HSD17B41
chr5:118860924p.G601C,HSD17B41
chr5:118810155p.D76N,HSD17B41
chr5:118865604p.P340A,HSD17B41
chr5:118824931p.P495L,HSD17B41

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 HSD17B4 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 HSD17B4

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

AP3B1,C5orf15,KIAA0825,TRAPPC13,COMMD10,DCTN4,DTWD2,
FAM114A2,FBXL17,GIN1,HSD17B4,MATR3,MFAP3,MSH3,
NUDT12,PGGT1B,PJA2,POLK,TMED7,YTHDC2,ZFYVE16
ACO1,AHCYL1,ASAH1,BTD,FAM213A,CAT,HNMT,
HRASLS5,HSD17B4,OXCT1,PARVA,PEX19,PLIN1,RHOBTB3,
RRAGC,RTN3,SEPT11,SLC25A16,SNX5,SORT1,VKORC1L1

ALDH7A1,AP3B1,CDC23,GLB1,HMGCR,HSD17B4,HSPA9,
LARS,LYRM7,MCCC2,MRPS27,MRPS36,PAPD4,RIOK2,
SKIV2L2,SLC25A46,SLC30A5,SRFBP1,TAF9,TMEM161B,UBE2D2
ALG6,ANKEF1,ATP6V1A,CCDC47,DARS2,FAM81A,FAR2,
GMDS,HSD17B4,IDH1,MCCC2,MTIF2,NARS,ORC2,
PHKB,SH2D4A,SRPK1,STAMBPL1,STARD7,STT3B,TM9SF2
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 HSD17B4
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 4approved; nutraceuticalNADH
DB01907hydroxysteroid (17-beta) dehydrogenase 4experimentalNicotinamide-Adenine-Dinucleotide
DB03192hydroxysteroid (17-beta) dehydrogenase 4experimental3r-Hydroxydecanoyl-Coa
DB00145hydroxysteroid (17-beta) dehydrogenase 4approved; nutraceuticalGlycine


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Cross referenced IDs for HSD17B4
* 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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