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 RETSAT
Basic gene info.Gene symbolRETSAT
Gene nameretinol saturase (all-trans-retinol 13,14-reductase)
Synonyms-
CytomapUCSC genome browser: 2p11.2
Genomic locationchr2 :85569077-85581821
Type of geneprotein-coding
RefGenesNM_017750.3,
Ensembl idENSG00000042445
DescriptionPPAR-alpha-regulated and starvation-induced gene proteinall-trans-13,14-dihydroretinol saturaseall-trans-retinol 13,14-reductase
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000042445
HPRD : 07893
Vega : OTTHUMG00000154611
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RETSAT
BioGPS: 54884
Gene Expression Atlas: ENSG00000042445
The Human Protein Atlas: ENSG00000042445
PathwayNCI Pathway Interaction Database: RETSAT
KEGG: RETSAT
REACTOME: RETSAT
ConsensusPathDB
Pathway Commons: RETSAT
MetabolismMetaCyc: RETSAT
HUMANCyc: RETSAT
RegulationEnsembl's Regulation: ENSG00000042445
miRBase: chr2 :85,569,077-85,581,821
TargetScan: NM_017750
cisRED: ENSG00000042445
ContextiHOP: RETSAT
cancer metabolism search in PubMed: RETSAT
UCL Cancer Institute: RETSAT
Assigned class in ccmGDBC

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

Mutations for RETSAT
* 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 RETSAT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW847517TMEM151B118464427240244272822RETSAT17732928557095985571111
CA312858RETSAT1713028556922085569333HLA-DRB512632363248514632485343

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=46)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr2:85570849-85570849p.G536R5
chr2:85571228-85571228p.A476G5
chr2:85570857-85570857p.A533V4
chr2:85578126-85578126p.R125H4
chr2:85577263-85577263p.P233P3
chr2:85571180-85571180p.S492F3
chr2:85571210-85571210p.R482L2
chr2:85581487-85581487p.K48K2
chr2:85571225-85571225p.E477G2
chr2:85570442-85570442p.A586T2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 5  1112 1111 197 9
# mutation22 5  1111 1211 198 9
nonsynonymous SNV22 4    11 811 177 7
synonymous SNV   1  11   4    21 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
chr2:85578126p.R369C2
chr2:85573110p.S492F2
chr2:85576630p.R125L2
chr2:85571180p.P292S2
chr2:85571194p.S253F1
chr2:85573154p.L12L1
chr2:85577189p.R543C1
chr2:85570768p.L364L1
chr2:85571218p.H207N1
chr2:85578130p.L9L1

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 RETSAT 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 RETSAT

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

ALCAM,AR,ARHGEF38,ATP13A4,APMAP,RHOV___CHP1,CROT,
ELMOD3,FZD4,GGCX,IQGAP2,MAN2B2,MPV17L,PCYOX1,
RETSAT,RNF103,SCP2,SLC9A1,TMEM62,TMEM63C,TMEM86A
ACO1,AIFM2,AOC2,AOC3,BTD,DHDDS,EHD2,
GPD1,HEPN1,MGLL,MRAS,MYO1C,PLIN1,PLXNA4,
PYGL,RDH5,RETSAT,TFE3,TK2,TLN2,VKORC1L1

ABHD3,B3GALT5,BTNL3,BTNL8,CDHR5,DHRS9,GDPD3,
GPA33,GPT,LIMA1,MALL,MMP28,P2RX4,PTPRH,
RETSAT,SDCBP2,SLC41A2,STYK1,TMPRSS2,TSPAN1,VILL
ACOX1,ALDH18A1,APPL2,C1orf106,CDKN2B,RHOV___CHP1,ERBB3,
TMEM236,HNF4A,KALRN,MARVELD3,MAST2,MGAT4A,MYO1D,
PRKCD,PSEN1,RETSAT,RNF103,SLC22A5,SLC41A2,SPINT1
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 RETSAT
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
DB00162retinol saturase (all-trans-retinol 13,14-reductase)approved; nutraceuticalVitamin A


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Cross referenced IDs for RETSAT
* 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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