Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	HSD17B3
	Gene name	hydroxysteroid (17-beta) dehydrogenase 3
	Synonyms	EDH17B3\|SDR12C2
	Cytomap	UCSC genome browser: 9q22
	Genomic location	chr9 :98997588-99064434
	Type of gene	protein-coding
	RefGenes	NM_000197.1,
	Ensembl id	ENSG00000130948
	Description	17-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 date	20141207
dbXrefs	MIM : 605573
	HGNC : HGNC
	Ensembl : ENSG00000130948
	HPRD : 05716
	Vega : OTTHUMG00000020292
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HSD17B3
	BioGPS: 3293
	Gene Expression Atlas: ENSG00000130948
	The Human Protein Atlas: ENSG00000130948
Pathway	NCI Pathway Interaction Database: HSD17B3
	KEGG: HSD17B3
	REACTOME: HSD17B3
	ConsensusPathDB
	Pathway Commons: HSD17B3
Metabolism	MetaCyc: HSD17B3
	HUMANCyc: HSD17B3
Regulation	Ensembl's Regulation: ENSG00000130948
	miRBase: chr9 :98,997,588-99,064,434
	TargetScan: NM_000197
	cisRED: ENSG00000130948
Context	iHOP: HSD17B3
	cancer metabolism search in PubMed: HSD17B3
	UCL Cancer Institute: HSD17B3
Assigned class in ccmGDB	C

Top

Phenotypic Information for HSD17B3(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: HSD17B3
	MedGen: HSD17B3 (Human Medical Genetics with Condition)
	ClinVar: HSD17B3
Phenotype	MGI: HSD17B3 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

Top

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	HSD17B3	chr9	99045702	99045722	SLC35D2	chr9	99100996	99101016
ovary	HSD17B3	chr9	99059287	99059307		chr9	98926204	98926224

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HSD17B3 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

Top

SNV 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

Top

Somatic 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.

Top

Top 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 position	Mutation(aa)	Unique sampleID count
chr9:99007679-99007679	p.S185F	3
chr9:99007682-99007682	p.S184Y	3
chr9:99060732-99060732	p.A56V	2
chr9:99064321-99064321	p.A22A	2
chr9:98997817-98997817	p.F286F	2
chr9:99006625-99006625	p.E220*	2
chr9:99006664-99006664	p.A207T	2
chr9:99060718-99060718	p.G61W	2
chr9:99007662-99007662	p.P191S	1
chr9:99013729-99013729	p.H142Y	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1		1	1		1					5		1		1	8	1		6
# mutation	1	1		1	1		1					5		1		1	8	1		6
nonsynonymous SNV	1			1	1		1					3				1	5	1		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])

Top

Top 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 Position	Mutation(aa)	Unique sampleID count
chr9:99013747	p.K210K	1
chr9:99003133	p.A22T	1
chr9:99015130	p.P191S	1
chr9:99003166	p.L5L	1
chr9:99015147	p.E173K	1
chr9:99003178	p.H155N	1
chr9:99015188	p.I150I	1
chr9:99006653	p.E149K	1
chr9:99015189	p.H142Y	1
chr9:99007662	p.F286L	1

Other 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

Copy 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]

Top

Gene Expression for HSD17B3

Gene 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.

Differential 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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

Gene-Gene Network Information

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for HSD17B3

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00157	hydroxysteroid (17-beta) dehydrogenase 3	approved; nutraceutical	NADH
DB00396	hydroxysteroid (17-beta) dehydrogenase 3	approved	Progesterone
DB00624	hydroxysteroid (17-beta) dehydrogenase 3	approved; investigational	Testosterone

Top

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