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 SRD5A3
Basic gene info.Gene symbolSRD5A3
Gene namesteroid 5 alpha-reductase 3
SynonymsCDG1P|CDG1Q|KRIZI|SRD5A2L|SRD5A2L1
CytomapUCSC genome browser: 4q12
Genomic locationchr4 :56212387-56239266
Type of geneprotein-coding
RefGenesNM_024592.4,
Ensembl idENSG00000128039
Description3-oxo-5-alpha-steroid 4-dehydrogenase 3S5AR 3SR type 3polyprenol reductaseprobable polyprenol reductase
Modification date20141219
dbXrefs MIM : 611715
HGNC : HGNC
Ensembl : ENSG00000128039
HPRD : 07825
Vega : OTTHUMG00000128733
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SRD5A3
BioGPS: 79644
Gene Expression Atlas: ENSG00000128039
The Human Protein Atlas: ENSG00000128039
PathwayNCI Pathway Interaction Database: SRD5A3
KEGG: SRD5A3
REACTOME: SRD5A3
ConsensusPathDB
Pathway Commons: SRD5A3
MetabolismMetaCyc: SRD5A3
HUMANCyc: SRD5A3
RegulationEnsembl's Regulation: ENSG00000128039
miRBase: chr4 :56,212,387-56,239,266
TargetScan: NM_024592
cisRED: ENSG00000128039
ContextiHOP: SRD5A3
cancer metabolism search in PubMed: SRD5A3
UCL Cancer Institute: SRD5A3
Assigned class in ccmGDBC

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Phenotypic Information for SRD5A3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SRD5A3
Familial Cancer Database: SRD5A3
* 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: SRD5A3
MedGen: SRD5A3 (Human Medical Genetics with Condition)
ClinVar: SRD5A3
PhenotypeMGI: SRD5A3 (International Mouse Phenotyping Consortium)
PhenomicDB: SRD5A3

Mutations for SRD5A3
* 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 SRD5A3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI906091SRD5A318745622556456225650SRD5A38424145623024056230397

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample 2               
GAIN (# sample) 2               
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)

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=19)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr4:56230311-56230311p.F145F3
chr4:56212685-56212685p.S61L2
chr4:56236183-56236183p.L294L2
chr4:56225634-56225634p.L115I2
chr4:56236065-56236065p.N255I2
chr4:56230247-56230247p.E124G1
chr4:56236091-56236091p.V264I1
chr4:56230251-56230251p.L125L1
chr4:56236103-56236103p.V268I1
chr4:56225519-56225519p.F76L1

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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
# sample1 231 2 1  82   24 3
# mutation1 231 2 1  82   24 3
nonsynonymous SNV  11  1    42   12 3
synonymous SNV1 121 1 1  4    12  
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
chr4:56230311p.L294L2
chr4:56225634p.L115F2
chr4:56236183p.F145F2
chr4:56230251p.K56K1
chr4:56236191p.C238S1
chr4:56212671p.S61L1
chr4:56236195p.E249K1
chr4:56212685p.P63P1
chr4:56230347p.V264I1
chr4:56236243p.S83P1

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 SRD5A3 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 SRD5A3

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

ABCC12,MAB21L3,HILPDA,DBI,ERO1L,FABP6,FUT3,
GGCT,GGT1,GGTLC1,IDH1,KMO,KYNU,MUCL1,
PDZK1IP1,MSMO1,SERHL2,SLC31A1,SRD5A3,TMEM165,TRPV6
AGA,C14orf1,COMMD7,DERL2,DPAGT1,G6PC3,GGPS1,
HIST1H2BK,MPDU1,MPV17,ORMDL2,PGRMC1,PRDX1,SLC50A1,
REEP5,SLC25A17,SPCS1,SRD5A3,TMBIM6,TMCO1,TMEM59

AGR2,ANG,ARFGAP3,TMEM263,GSKIP,CD55,CHST5,
CREB3L1,FAM177B,GALNT3,GALNT7,KDELR3,MLPH,REG4,
RNASE4,SDR16C5,SLC35A1,SRD5A3,TC2N,TSPAN13,UAP1
ACAT2,C20orf141,NCOR1P1,BPIFA2,CLEC4G,FDFT1,GPX5,
KPRP,LCE2C,MEPE,CHODL-AS1,OR1F2P,OR2D2,PGLYRP3,
PLA2G4D,RARRES1,SNORA79,SPATS1,SRD5A3,TRIM6-TRIM34,ZSWIM2
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 SRD5A3


There's no related Drug.
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Cross referenced IDs for SRD5A3
* 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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