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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for RLBP1
check button Gene summary
Basic gene informationGene symbolRLBP1
Gene nameretinaldehyde binding protein 1
SynonymsCRALBP
CytomapUCSC genome browser: 15q26
Type of geneprotein-coding
RefGenesNM_000326.4,
Descriptioncellular retinaldehyde-binding proteincellular retinaldehyde-binding protein-1retinaldehyde-binding protein 1
Modification date20141219
dbXrefs MIM : 180090
HGNC : HGNC
Ensembl : ENSG00000140522
HPRD : 01572
Vega : OTTHUMG00000172884
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RLBP1
BioGPS: 6017
PathwayNCI Pathway Interaction Database: RLBP1
KEGG: RLBP1
REACTOME: RLBP1
Pathway Commons: RLBP1
ContextiHOP: RLBP1
ligand binding site mutation search in PubMed: RLBP1
UCL Cancer Institute: RLBP1
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesHPA,TiGER
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)BrainEye
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)GBM,LGGUVM
Reference showing the relevant tissue of RLBP1
Description by TissGene annotationsProtective TissGene in RFS
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID


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TissGeneExp for RLBP1

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
STAD-1.687611202-0.651264327-1.0363468750.003320.013852839
COAD-1.547298221-0.359190529-1.1881076920.0004780.001483425


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TissGene-miRNA for RLBP1

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for RLBP1
TissGeneSNV for RLBP1

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)

* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.D288GLIHC1
p.R42HBLCA1
p.R234QSTAD1
p.R101HPRAD1
p.V158ISTAD1
p.Q309RCOAD1
p.A72VBLCA1
p.L148IPAAD1
p.E282VSKCM1
p.R64*CESC1
p.P36LTHYM1
p.D281NREAD1
p.P36LUCEC1
p.Y124*OV1
p.F99LUCEC1
p.E3KBRCA1
p.G307SSKCM1
p.E279KSKCM1
p.G77EKIRC1
p.F161SGBM1
p.V136LBLCA1
p.A102TSTAD1
p.G31RSKCM1
p.I176MBLCA1
p.R216QSKCM1
p.R103WSTAD1
p.E3DDLBC1
p.E54KCOAD1
p.E192VSKCM1
p.G4RSKCM1
p.L220ILUAD1
p.Q67KSTAD1
p.E164QBLCA1
p.G290RUCEC1
p.A85VPRAD1
p.M223IHNSC1
p.R64*HNSC1
p.A74VSTAD1
p.E78KSKCM1
p.L131QLUAD1
p.D50YUCEC1
p.N106SLIHC1
p.R9HCOAD1
p.G4ESKCM1
p.E170KBLCA1


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TissGeneCNV for RLBP1

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for RLBP1

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0ChiTaRsNAW28826RLBP1-RLBP1chr15:89762220chr15:89762211


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TissGeneNet for RLBP1

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)
BRCA (tumor)BRCA (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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COAD (tumor)COAD (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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HNSC (tumor)HNSC (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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KICH (tumor)KICH (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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KIRC (tumor)KIRC (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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KIRP (tumor)KIRP (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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LIHC (tumor)LIHC (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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LUAD (tumor)LUAD (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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LUSC (tumor)LUSC (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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PRAD (tumor)PRAD (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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STAD (tumor)STAD (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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THCA (tumor)THCA (normal)
RLBP1, SLC9A3R1, RDH5 (tumor)RLBP1, SLC9A3R1, RDH5 (normal)
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TissGeneProg for RLBP1

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)

* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for RLBP1
TissGeneDrug for RLBP1

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status
DB00162Vitamin ASmall moleculeApproved|Nutraceutical|Vet_approved


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TissGeneDisease for RLBP1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C1405854Retinitis punctata albescens (disorder)12BeFree,CLINVAR,GAD
umls:C0035334Retinitis Pigmentosa7BeFree,CTD_human,GAD,LHGDN,ORPHANET,UNIPROT
umls:C0339526Autosomal recessive retinitis pigmentosa7BeFree
umls:C0035309Retinal Diseases4BeFree,GAD
umls:C0311338Fundus Albipunctatus3BeFree,CLINVAR,CTD_human,ORPHANET,UNIPROT
umls:C0854723Retinal Dystrophies3BeFree
umls:C0035304Retinal Degeneration2BeFree
umls:C0035333Retinitis2LHGDN
umls:C0015398Eye Diseases, Hereditary1CTD_human
umls:C0032580Adenomatous Polyposis Coli1BeFree
umls:C0036341Schizophrenia1LHGDN
umls:C0042164Uveitis1LHGDN
umls:C0730290Cone dystrophy1BeFree
umls:C1260959Drusen1BeFree
umls:C1843815Newfoundland Rod-Cone Dystrophy1BeFree,CLINVAR,CTD_human
umls:C1843816Bothnia Retinal Dystrophy1CLINVAR,CTD_human,MGD,ORPHANET,UNIPROT