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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 CRABP1
check button Gene summary
Basic gene informationGene symbolCRABP1
Gene namecellular retinoic acid binding protein 1
SynonymsCRABP|CRABP-I|CRABPI|RBP5
CytomapUCSC genome browser: 15q24
Type of geneprotein-coding
RefGenesNM_004378.2,
Descriptioncellular retinoic acid-binding protein 1cellular retinoic acid-binding protein I
Modification date20141207
dbXrefs MIM : 180230
HGNC : HGNC
Ensembl : ENSG00000166426
HPRD : 07520
Vega : OTTHUMG00000143862
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_CRABP1
BioGPS: 1381
PathwayNCI Pathway Interaction Database: CRABP1
KEGG: CRABP1
REACTOME: CRABP1
Pathway Commons: CRABP1
ContextiHOP: CRABP1
ligand binding site mutation search in PubMed: CRABP1
UCL Cancer Institute: CRABP1
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)OvaryThyroid glandEye
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)OVTHCAUVM
Reference showing the relevant tissue of CRABP1
Description by TissGene annotations
* 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 CRABP1

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
LUSC-0.010856051-3.0443815413.033525492.81E-088.39E-08
BRCA0.9493241873.191677696-2.2423535092.61E-088.29E-08
COAD-1.7433354621.033718384-2.7770538468.73E-097.84E-08
KIRP-3.9818479621.809008288-5.790856251.66E-144.14E-13
PRAD-1.7802220010.153729922-1.9339519235.37E-063.24E-05
THCA3.1601433517.256095894-4.0959525421.17E-162.06E-15
LUAD-1.2543596-3.4437923592.1894327594.52E-071.57E-06
KIRC-3.104338241.109181204-4.2135194441.33E-191.01E-18
HNSC-0.13973431.259647096-1.3993813950.001380.004480519
KICH-1.7290694620.759114538-2.4881840.001360.002876622


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TissGene-miRNA for CRABP1

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 CRABP1
TissGeneSNV for CRABP1

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.W110RLUAD1
p.I133VBLCA1
p.K54NSKCM1
p.T97MLUAD1
p.G69RUCS1
p.D117NCOAD1
p.P106RTHYM1
p.R60HUCEC1
p.R83TBRCA1
p.V59ASTAD1
p.K81EUCEC1
p.G69EBLCA1
p.G105VLUAD1
p.D49NREAD1
p.D126NLUSC1
p.A35VSTAD1


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TissGeneCNV for CRABP1

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 CRABP1

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
Chimerdb3.0FusionScanLUADTCGA-86-7713-01APDE4D-CRABP1In-Framechr5:58334685chr15:78640268
Chimerdb3.0TopHat-FusionLUADTCGA-86-7713-01APDE4D-CRABP1In-Framechr5:58334685chr15:78640268
TCGAfusionPortalPRADALUADTCGA-86-7713-01APDE4D-CRABP1In-frameChr5:58334686Chr15:78640269


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TissGeneNet for CRABP1

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)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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COAD (tumor)COAD (normal)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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HNSC (tumor)HNSC (normal)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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KICH (tumor)KICH (normal)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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KIRC (tumor)KIRC (normal)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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KIRP (tumor)KIRP (normal)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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LIHC (tumor)LIHC (normal)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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LUAD (tumor)LUAD (normal)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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LUSC (tumor)LUSC (normal)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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PRAD (tumor)PRAD (normal)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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STAD (tumor)STAD (normal)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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THCA (tumor)THCA (normal)
CRABP1, TRA2A, MPP3 (tumor)CRABP1, TRA2A, MPP3 (normal)
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TissGeneProg for CRABP1

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 CRABP1
TissGeneDrug for CRABP1

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status


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TissGeneDisease for CRABP1

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0001430Adenoma2BeFree
umls:C0003873Rheumatoid Arthritis2BeFree
umls:C0023467Leukemia, Myelocytic, Acute2BeFree
umls:C0023487Acute Promyelocytic Leukemia2BeFree
umls:C0040136Thyroid Neoplasm2LHGDN
umls:C0238463Papillary thyroid carcinoma2BeFree
umls:C0596263Carcinogenesis2BeFree
umls:C0007134Renal Cell Carcinoma1BeFree,CTD_human,LHGDN
umls:C0007137Squamous cell carcinoma1BeFree
umls:C0009402Colorectal Carcinoma1BeFree
umls:C0022548Keloid1CTD_human
umls:C0023267Fibroid Tumor1BeFree
umls:C0023903Liver neoplasms1CTD_human
umls:C0026654Moyamoya Disease1LHGDN
umls:C0027794Neural Tube Defects1GAD
umls:C0027819Neuroblastoma1BeFree
umls:C0042133Uterine Fibroids1BeFree
umls:C0279626Squamous cell carcinoma of esophagus1BeFree,CTD_human
umls:C0339143Thyroid associated opthalmopathies1BeFree
umls:C0686619Secondary malignant neoplasm of lymph node1BeFree
umls:C0700095Central neuroblastoma1BeFree
umls:C1153706Endometrial adenocarcinoma1BeFree
umls:C1168401Squamous cell carcinoma of the head and neck1BeFree
umls:C1527249Colorectal Cancer1BeFree
umls:C3811653Experimental Organism Basal Cell Carcinoma1BeFree