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 HSD17B10
Basic gene info.Gene symbolHSD17B10
Gene namehydroxysteroid (17-beta) dehydrogenase 10
Synonyms17b-HSD10|ABAD|CAMR|DUPXp11.22|ERAB|HADH2|HCD2|MHBD|MRPP2|MRX17|MRX31|MRXS10|SCHAD|SDR5C1
CytomapUCSC genome browser: Xp11.2
Genomic locationchrX :53458205-53461323
Type of geneprotein-coding
RefGenesNM_001037811.2,
NM_004493.2,
Ensembl idENSG00000268188
Description3-hydroxy-2-methylbutyryl-CoA dehydrogenase3-hydroxyacyl-CoA dehydrogenase type-2AB-binding alcohol dehydrogenaseamyloid-beta peptide binding alcohol dehydrogenaseendoplasmic reticulum-associated amyloid beta-peptide-binding proteinmitochondrial RNas
Modification date20141207
dbXrefs MIM : 300256
HGNC : HGNC
Ensembl : ENSG00000072506
HPRD : 02223
Vega : OTTHUMG00000021612
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HSD17B10
BioGPS: 3028
Gene Expression Atlas: ENSG00000268188
The Human Protein Atlas: ENSG00000268188
PathwayNCI Pathway Interaction Database: HSD17B10
KEGG: HSD17B10
REACTOME: HSD17B10
ConsensusPathDB
Pathway Commons: HSD17B10
MetabolismMetaCyc: HSD17B10
HUMANCyc: HSD17B10
RegulationEnsembl's Regulation: ENSG00000268188
miRBase: chrX :53,458,205-53,461,323
TargetScan: NM_001037811
cisRED: ENSG00000268188
ContextiHOP: HSD17B10
cancer metabolism search in PubMed: HSD17B10
UCL Cancer Institute: HSD17B10
Assigned class in ccmGDBC

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Phenotypic Information for HSD17B10(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HSD17B10
Familial Cancer Database: HSD17B10
* 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_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HSD17B10
MedGen: HSD17B10 (Human Medical Genetics with Condition)
ClinVar: HSD17B10
PhenotypeMGI: HSD17B10 (International Mouse Phenotyping Consortium)
PhenomicDB: HSD17B10

Mutations for HSD17B10
* 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 HSD17B10 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF756615HSD17B101254X5345893653459321APEX1247348142092344920923550

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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=18)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr23:53459205-53459205p.R116Q2
chr23:53460830-53460830p.L11M1
chr23:53458487-53458487p.L217L1
chr23:53459279-53459279p.C91W1
chr23:53460832-53460832p.G10D1
chr23:53458945-53458945p.F159F1
chr23:53459334-53459334p.T73K1
chr23:53461277-53461277p.R6W1
chr23:53458992-53458992p.G144R1
chr23:53459338-53459338p.Q72*1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 21      21   2  5
# mutation 1 21      21   2  7
nonsynonymous SNV 1 11      2    2  5
synonymous SNV   1        1      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
chrX:53458992p.R116Q,HSD17B101
chrX:53460832p.T110S,HSD17B101
chrX:53459013p.T100M,HSD17B101
chrX:53461282p.C91W,HSD17B101
chrX:53459056p.Q50R,HSD17B101
chrX:53459201p.G34E,HSD17B101
chrX:53459205p.A13T,HSD17B101
chrX:53459223p.G10D,HSD17B101
chrX:53459253p.A4V,HSD17B101
chrX:53459279p.A230V,HSD17B101

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 HSD17B10 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 HSD17B10

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

CCDC124,DPM3,EBP,FAM50A,HSD17B10,LSM7,MPST,
MRPL52,MRPS12,NDUFA11,NDUFB11,NDUFB2,NDUFB7,POLR2I,
PQBP1,RBM10,RBM42,SDHAF1,TIMM17B,TSR2,UXT
AURKAIP1,BSG,CCDC106,CHMP2A,CLPP,FIS1,GRHPR,
HSD17B10,IDH3G,ILVBL,MPST,MRPL24,MRPL54,MTX1,
PEX16,PLEKHJ1,SNF8,TP53I13,TUFM,UBXN6,USE1

AIFM1,APEX2,CCDC22,CXorf40A,EBP,EMD,FAM58A,
FTSJ1,HAUS7,HDAC8,HSD17B10,LAGE3,CMC4,NAA10,
NDUFB11,PDZD11,PQBP1,SUV39H1,TIMM17B,TIMM8A,UXT
CCDC167,DCUN1D5,EBNA1BP2,EIF2S2,EIF3I,EIF5A,EIF5AL1,
HSD17B10,NAA10,NHP2,NME1,NPM3,NUTF2,NABP2,
PARK7,PPIH,PRMT1,PSMA7,PSMB6,PSMC3,RAN
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 HSD17B10
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 10approved; nutraceuticalNADH
DB01907hydroxysteroid (17-beta) dehydrogenase 10experimentalNicotinamide-Adenine-Dinucleotide
DB02820hydroxysteroid (17-beta) dehydrogenase 10experimental1-Azepan-1-Yl-2-Phenyl-2-(4-Thioxo-1,4-Dihydro-Pyrazolo[3,4-D]Pyrimidin-5-Yl)Ethanone Adduct


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Cross referenced IDs for HSD17B10
* 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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