Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 RXRA
Basic gene info.Gene symbolRXRA
Gene nameretinoid X receptor, alpha
SynonymsNR2B1
CytomapUCSC genome browser: 9q34.3
Genomic locationchr9 :137218315-137332431
Type of geneprotein-coding
RefGenesNM_001291920.1,
NM_001291921.1,NM_002957.5,
Ensembl idENSG00000269571
Descriptionnuclear receptor subfamily 2 group B member 1retinoic acid receptor RXR-alpharetinoid X nuclear receptor alpha
Modification date20141222
dbXrefs MIM : 180245
HGNC : HGNC
HPRD : 01577
ProteinUniProt: P19793
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RXRA
BioGPS: 6256
Gene Expression Atlas: ENSG00000269571
The Human Protein Atlas: ENSG00000269571
PathwayNCI Pathway Interaction Database: RXRA
KEGG: RXRA
REACTOME: RXRA
ConsensusPathDB
Pathway Commons: RXRA
MetabolismMetaCyc: RXRA
HUMANCyc: RXRA
RegulationEnsembl's Regulation: ENSG00000269571
miRBase: chr9 :137,218,315-137,332,431
TargetScan: NM_001291920
cisRED: ENSG00000269571
ContextiHOP: RXRA
cancer metabolism search in PubMed: RXRA
UCL Cancer Institute: RXRA
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of RXRA in cancer cell metabolism1. Deepa PR, Vandhana S, Krishnakumar S (2013) Fatty acid synthase inhibition induces differential expression of genes involved in apoptosis and cell proliferation in ocular cancer cells. Nutrition and cancer 65: 311-316. go to article

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Phenotypic Information for RXRA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RXRA
Familial Cancer Database: RXRA
* 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 BLCA 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12965.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 180245; gene.
Orphanet
DiseaseKEGG Disease: RXRA
MedGen: RXRA (Human Medical Genetics with Condition)
ClinVar: RXRA
PhenotypeMGI: RXRA (International Mouse Phenotyping Consortium)
PhenomicDB: RXRA

Mutations for RXRA
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastRXRAchr9137221922137222322LUC7L3chr174881902748819427
ovaryRXRAchr9137303708137303728RXRAchr9137305107137305127
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RXRA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW881282RXRA302919137328444137328705RXRA2883689137325987137328326
AW881216RXRA82769137328437137328705RXRA2733609137325987137328333
BM978893RXRA191079137332343137332431LRBA1066104151283588151284092

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 # sample1       1        
GAIN (# sample)                 
LOSS (# sample)1       1        
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=16

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=16)
Stat. for Deletions
(# total SNVs=2)
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
chr9:137328351-137328351p.S427F16
chr9:137300840-137300840p.T162M2
chr9:137309085-137309085p.P231L2
chr9:137309139-137309139p.Y249F2
chr9:137320990-137320990p.R316L2
chr9:137309140-137309140p.Y249Y2
chr9:137328442-137328442p.A457A2
chr9:137328331-137328331p.L420L2
chr9:137300040-137300040p.P109S2
chr9:137309028-137309028p.G212D2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample131 82 4 1  151  3614
# mutation71 82 4 1  151  3714
nonsynonymous SNV61 62 4    121  35 2
synonymous SNV1  2    1   3    212
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
chr9:137328351p.S330F,RXRA7
chr9:137320990p.R219H,RXRA2
chr9:137293649p.G332V,RXRA1
chr9:137328340p.P3P,RXRA1
chr9:137300876p.R205Q,RXRA1
chr9:137321021p.G346E,RXRA1
chr9:137293679p.I10I,RXRA1
chr9:137328348p.P349S,RXRA1
chr9:137300887p.P12S,RXRA1
chr9:137321027p.S220F,RXRA1

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 RXRA 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 RXRA

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

ABCA2,ALAD,ANAPC2,PRRC2B,CACFD1,EHMT1,FAM73B,
JMJD7-PLA2G4B,PPP1R26,MED22,MXD4,NDOR1,PKD1,PPP2R4,
RGS12,RXRA,TAOK2,TBC1D13,TNRC18,USP20,ZER1
ABCD1,ACADS,AGPAT2,ALDH2,ANXA6,ADIRF,C14orf180,
CAMK1,CEBPA,COL4A2,CSPG4,GYPC,ITGA7,LOC80054,
PLA2G16,PNPLA2,POLR2E,PPP1R1A,RXRA,ST6GALNAC6,TMEM132C

PRRC2B,MIR600HG,CASZ1,CIZ1,NELFB,CORO2A,DAB2IP,
DENND1A,EHMT1,EXD3,FAM73B,GPR107,ARHGAP35,KIAA0368,
PPP1R26,RAPGEF1,RXRA,TBC1D13,TSC1,WDR37,ZER1
AGPAT3,ARHGEF11,ATG9A,BAHD1,BTBD9,CLIP2,DGCR2,
ERBB2,ERBB3,ARHGAP35,KIAA1522,MAST2,N4BP1,PTPRF,
RAB40C,RNPEPL1,RXRA,SIPA1L3,SPINT1,SPPL3,TNIP1
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 RXRA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P19793; -.
ChemistryChEMBL CHEMBL2363071; -.
ChemistryGuidetoPHARMACOLOGY 610; -.
Organism-specific databasesPharmGKB PA34890; -.
Organism-specific databasesCTD 6256; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00210retinoid X receptor, alphaapprovedAdapalene
DB00307retinoid X receptor, alphaapproved; investigationalBexarotene
DB00459retinoid X receptor, alphaapprovedAcitretin
DB00523retinoid X receptor, alphaapproved; investigationalAlitretinoin
DB00749retinoid X receptor, alphaapproved; investigationalEtodolac
DB00926retinoid X receptor, alphawithdrawnEtretinate
DB07557retinoid X receptor, alphaexperimental(5BETA)-PREGNANE-3,20-DIONE
DB07863retinoid X receptor, alphaexperimental2-chloro-5-nitro-N-phenylbenzamide
DB08063retinoid X receptor, alphaexperimental1-BENZYL-3-(4-METHOXYPHENYLAMINO)-4-PHENYLPYRROLE-2,5-DIONE
DB08402retinoid X receptor, alphaexperimental2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID
DB08601retinoid X receptor, alphaexperimentaltributylstannanyl
DB00755retinoid X receptor, alphaapproved; nutraceutical; investigationalTretinoin
DB00741retinoid X receptor, alphaapprovedHydrocortisone
DB01132retinoid X receptor, alphaapproved; investigationalPioglitazone
DB00412retinoid X receptor, alphaapproved; investigationalRosiglitazone
DB00197retinoid X receptor, alphawithdrawnTroglitazone


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Cross referenced IDs for RXRA
* 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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