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 DHRS4
Basic gene info.Gene symbolDHRS4
Gene namedehydrogenase/reductase (SDR family) member 4
SynonymsCR|NRDR|PHCR|PSCD|SCAD-SRL|SDR-SRL|SDR25C1|SDR25C2
CytomapUCSC genome browser: 14q11.2
Genomic locationchr14 :24422964-24438488
Type of geneprotein-coding
RefGenesNM_001282987.1,
NM_001282988.1,NM_001282989.1,NM_001282990.1,NM_001282991.1,
NM_021004.3,
Ensembl idENSG00000157326
DescriptionNADPH-dependent carbonyl reductase/NADP-retinol dehydrogenaseNADPH-dependent retinol dehydrogenase/reductasedehydrogenase/reductase (SDR family) member 4 like 2Adehydrogenase/reductase SDR family member 4peroxisomal short-chain alcohol dehydrogenases
Modification date20141207
dbXrefs MIM : 611596
HGNC : HGNC
Ensembl : ENSG00000157326
HPRD : 07484
Vega : OTTHUMG00000028777
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_DHRS4
BioGPS: 10901
Gene Expression Atlas: ENSG00000157326
The Human Protein Atlas: ENSG00000157326
PathwayNCI Pathway Interaction Database: DHRS4
KEGG: DHRS4
REACTOME: DHRS4
ConsensusPathDB
Pathway Commons: DHRS4
MetabolismMetaCyc: DHRS4
HUMANCyc: DHRS4
RegulationEnsembl's Regulation: ENSG00000157326
miRBase: chr14 :24,422,964-24,438,488
TargetScan: NM_001282987
cisRED: ENSG00000157326
ContextiHOP: DHRS4
cancer metabolism search in PubMed: DHRS4
UCL Cancer Institute: DHRS4
Assigned class in ccmGDBC

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Phenotypic Information for DHRS4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: DHRS4
Familial Cancer Database: DHRS4
* 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
KEGG_RETINOL_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: DHRS4
MedGen: DHRS4 (Human Medical Genetics with Condition)
ClinVar: DHRS4
PhenotypeMGI: DHRS4 (International Mouse Phenotyping Consortium)
PhenomicDB: DHRS4

Mutations for DHRS4
* 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 DHRS4 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=5

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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
chr14:24424420-24424420p.T102M5
chr14:24424255-24424255p.A47V2
chr14:24423007-24423007p.A4T2
chr14:24424346-24424346p.Q77Q2
chr14:24435560-24435560p.L200L1
chr14:24424253-24424253p.F46F1
chr14:24429135-24429135p.D111N1
chr14:24435564-24435564p.P202S1
chr14:24429154-24429154p.A117V1
chr14:24435598-24435598p.G213E1

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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
# sample 1 3  1 31 311  1  1
# mutation 1 3  1 31 311  1  1
nonsynonymous SNV 1 2  1 21 111     1
synonymous SNV   1    1  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
chr14:24424420p.T102M,DHRS42
chr14:24424255p.A47V,DHRS42
chr14:24424278p.D55Y,DHRS41
chr14:24424292p.V59V,DHRS41
chr14:24424306p.R64Q,DHRS41
chr14:24424307p.R64R,DHRS41
chr14:24424404p.E97K,DHRS41
chr14:24435538p.T159N,DHRS41
chr14:24423018p.L166L,DHRS41
chr14:24435560p.G179E,DHRS41

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 DHRS4 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 DHRS4

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

C19orf24,CHCHD5,COQ4,DCXR,DHRS4,DHRS4L1,DHRS4L2,
EDF1,ENDOG,EMC9,FKBP2,GSTZ1,MMAB,MPG,
MRPL41,MRPL54,PHPT1,SDSL,SIL1,TP53TG1,UQCR11
AUP1,AURKAIP1,ELP6,CHMP2A,DDRGK1,DHRS4,DHRS4L2,
IDH3G,MEA1,MED11,MRPL28,NAA10,NUDC,PMVK,
PSMD13,PSMD9,RAB1B,SPR,TEX264,TMEM147,TMEM187

C14orf166,C14orf2,CHCHD10,CHMP4A,CINP,DHRS4,DHRS4L1,
DHRS4L2,ENDOG,MZT2B,EMC9,GLRX5,GSTZ1,HAUS4,
MED11,NUDT8,OSGEP,PSMB5,PSMC1,RABGGTA,RPL36AL
ACY3,AKR1A1,CLDN15,CRIP1,CYP2J2,DAK,DDC,
DHRS4L2,F11,FBP1,GCHFR,MMEL1,MS4A15,OTC,
PRSS1,SLC25A15,SLC37A4,TIGD3,TMEM92,PRSS3P2,TTC36
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 DHRS4
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
DB00162dehydrogenase/reductase (SDR family) member 4approved; nutraceuticalVitamin A


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Cross referenced IDs for DHRS4
* 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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