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 HSD3B7
Basic gene info.Gene symbolHSD3B7
Gene namehydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7
SynonymsCBAS1|PFIC4|SDR11E3
CytomapUCSC genome browser: 16p11.2
Genomic locationchr16 :30996518-31000473
Type of geneprotein-coding
RefGenesNM_001142777.1,
NM_001142778.1,NM_025193.3,
Ensembl idENSG00000099377
Description3 beta-hydroxy-delta 5-C27-steroid oxidoreductase3 beta-hydroxysteroid dehydrogenase type 73 beta-hydroxysteroid dehydrogenase type VII3-beta-HSD VII3-beta-hydroxy-Delta(5)-C27 steroid oxidoreductaseC(27)-3BETA-HSDc(27) 3-beta-HSDcholest-5-ene-3-be
Modification date20141207
dbXrefs MIM : 607764
HGNC : HGNC
Ensembl : ENSG00000099377
HPRD : 09680
Vega : OTTHUMG00000132417
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HSD3B7
BioGPS: 80270
Gene Expression Atlas: ENSG00000099377
The Human Protein Atlas: ENSG00000099377
PathwayNCI Pathway Interaction Database: HSD3B7
KEGG: HSD3B7
REACTOME: HSD3B7
ConsensusPathDB
Pathway Commons: HSD3B7
MetabolismMetaCyc: HSD3B7
HUMANCyc: HSD3B7
RegulationEnsembl's Regulation: ENSG00000099377
miRBase: chr16 :30,996,518-31,000,473
TargetScan: NM_001142777
cisRED: ENSG00000099377
ContextiHOP: HSD3B7
cancer metabolism search in PubMed: HSD3B7
UCL Cancer Institute: HSD3B7
Assigned class in ccmGDBC

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Phenotypic Information for HSD3B7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HSD3B7
Familial Cancer Database: HSD3B7
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HSD3B7
MedGen: HSD3B7 (Human Medical Genetics with Condition)
ClinVar: HSD3B7
PhenotypeMGI: HSD3B7 (International Mouse Phenotyping Consortium)
PhenomicDB: HSD3B7

Mutations for HSD3B7
* 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 HSD3B7 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=6

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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
chr16:30999462-30999462p.R356R6
chr16:30998198-30998198p.R190L3
chr16:30999198-30999198p.Y268Y2
chr16:30999232-30999232p.G280*2
chr16:30997993-30997993p.E167K2
chr16:30999285-30999285p.F297F2
chr16:30999142-30999142p.T250A2
chr16:30997933-30997933p.E147K1
chr16:30999394-30999394p.S334G1
chr16:30998216-30998216p.G196V1

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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 5  1    3 1  5516
# mutation11 5  1    3 1  4516
nonsynonymous SNV1  4       3 1  3415
synonymous SNV 1 1  1         11 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
chr16:30999285p.F297F2
chr16:30997993p.E167K,HSD3B72
chr16:30999231p.H102Y,HSD3B71
chr16:30998163p.G254D1
chr16:30999249p.E103E,HSD3B71
chr16:30997441p.F258L1
chr16:30998197p.V112M,HSD3B71
chr16:30997507p.P264S1
chr16:30998198p.T119N,HSD3B71
chr16:30999362p.C279C1

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 HSD3B7 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 HSD3B7

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

ARMC5,BCKDK,CD2BP2,DECR2,FAM173A,FLYWCH2,GFER,
HSD3B7,JMJD8,MPG,NME3,NSMCE1,ORAI3,PHKG2,
PRR14,ROGDI,STX4,TMEM219,ZNF688,ZNF768,ZNF771
AP2A2,C1QA,CLEC3B,CST3,DBN1,DOK2,ECM1,
EMP3,FCGRT,FOLR2,GFRA2,COLGALT1,HSD3B7,MFRP,
MGAT1,NCF4,PRSS36,RENBP,S100A6,SH3BGRL3,TGFB1

BLVRA,CCDC109B,CCL4,ACKR4___CX3CR1,CD74,CDC42EP1,CTSW,
F12,GNLY,HSD3B7,IFI35,ODF3B,PARP9,PML,
PSMD9,PSME1,PSME2,RTP4,UBE2L6,USP18,ZMYND15
ACOT7,ASPA,PLEKHS1,EXOC3L4,C19orf12,CA9,ACKR4___CX3CR1,
CNDP2,DGKZ,RMDN3,GALK1,HSD3B7,LPGAT1,MLN,
ODF3B,SH3GL1,SHISA5,SHMT1,SLC25A22,TK2,UNC5CL
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 HSD3B7
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
DB00145hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7approved; nutraceuticalGlycine


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Cross referenced IDs for HSD3B7
* 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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