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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 RDH12
check button Gene summary
Basic gene informationGene symbolRDH12
Gene nameretinol dehydrogenase 12 (all-trans/9-cis/11-cis)
SynonymsLCA13|LCA3|RP53|SDR7C2
CytomapUCSC genome browser: 14q24.1
Type of geneprotein-coding
RefGenesNM_152443.2,
Descriptionall-trans and 9-cis retinol dehydrogenaseretinol dehydrogenase 12retinol dehydrogenase 12, all-trans and 9-cisshort chain dehydrogenase/reductase family 7C, member 2
Modification date20141219
dbXrefs MIM : 608830
HGNC : HGNC
Ensembl : ENSG00000139988
HPRD : 10585
Vega : OTTHUMG00000170032
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RDH12
BioGPS: 145226
PathwayNCI Pathway Interaction Database: RDH12
KEGG: RDH12
REACTOME: RDH12
Pathway Commons: RDH12
ContextiHOP: RDH12
ligand binding site mutation search in PubMed: RDH12
UCL Cancer Institute: RDH12
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)SkinEye
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)SKCMUVM
Reference showing the relevant tissue of RDH12
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
GO:0042572retinol metabolic process12226107
GO:0042572retinol metabolic process12226107


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TissGeneExp for RDH12

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
THCA1.2224089822.820229321-1.5978203391.64E-099.19E-09
KIRC1.2598332762.997184665-1.7373513891.57E-053.62E-05
LUSC0.476103864-0.9922745671.4683784318.25E-061.89E-05
KIRP0.2973447343.827457234-3.53011252.01E-081.45E-07
HNSC3.14592944.952775912-1.8068465120.005680.015070755
COAD-0.418998775-1.4425372371.0235384620.0002020.000681945
KICH-0.3005493912.399834609-2.7003845.87E-050.000160914
STAD1.0986666094.038760359-2.940093758.57E-060.000100911


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TissGene-miRNA for RDH12

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 RDH12
TissGeneSNV for RDH12

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.D187NSKCM2
p.A60TPRAD1
p.R314QUCEC1
p.S10FLUSC1
p.S190ILUAD1
p.K88NREAD1
p.D187NCOAD1
p.L153ILUAD1
p.E54KSKCM1
p.G46DHNSC1
p.R193HSTAD1
p.R57SLUSC1
p.G50SSTAD1
p.G39ALUAD1
p.G29ESKCM1
p.T299RBLCA1
p.F25LUCEC1
p.H148QKIRP1
p.M130TBRCA1
p.D101NREAD1
p.E110KKIRP1
p.G145RHNSC1
p.R62QSTAD1
p.G52CUCEC1
p.R302CUCEC1
p.E82KSKCM1
p.S90CBLCA1
p.T49MHNSC1
p.C245SCHOL1
p.V228LKIRP1
p.L277VHNSC1
p.L154ICOAD1


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TissGeneCNV for RDH12

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 RDH12

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


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TissGeneNet for RDH12

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)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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COAD (tumor)COAD (normal)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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HNSC (tumor)HNSC (normal)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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KICH (tumor)KICH (normal)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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KIRC (tumor)KIRC (normal)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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KIRP (tumor)KIRP (normal)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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LIHC (tumor)LIHC (normal)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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LUAD (tumor)LUAD (normal)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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LUSC (tumor)LUSC (normal)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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PRAD (tumor)PRAD (normal)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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STAD (tumor)STAD (normal)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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THCA (tumor)THCA (normal)
RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (tumor)RDH12, UBC, MAP1LC3A, BUB1, ANXA8 (normal)
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TissGeneProg for RDH12

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 RDH12
TissGeneDrug for RDH12

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 RDH12

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0339527Leber Congenital Amaurosis10BeFree,ORPHANET
umls:C0854723Retinal Dystrophies8BeFree,CTD_human
umls:C0035304Retinal Degeneration7BeFree,CTD_human
umls:C0035334Retinitis Pigmentosa6BeFree,CLINVAR,CTD_human,GAD,LHGDN,ORPHANET
umls:C2675186LEBER CONGENITAL AMAUROSIS 136CLINVAR,CTD_human,UNIPROT
umls:C0035309Retinal Diseases5BeFree,GAD
umls:C0456909Blind Vision3GAD,LHGDN
umls:C0020490Hyperopia1BeFree
umls:C0311338Fundus Albipunctatus1BeFree
umls:C0339525Autosomal dominant retinitis pigmentosa1BeFree
umls:C0917796Optic Atrophy, Hereditary, Leber1GAD
umls:C1301509Severe visual impairment1BeFree
umls:C1858677LEBER CONGENITAL AMAUROSIS 3 (disorder)0CTD_human
umls:C3150208RETINITIS PIGMENTOSA 530CLINVAR