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| TissGeneSummary for RDH12 |
 Gene summary |
| Basic gene information | Gene symbol | RDH12 |
| Gene name | retinol dehydrogenase 12 (all-trans/9-cis/11-cis) | |
| Synonyms | LCA13|LCA3|RP53|SDR7C2 | |
| Cytomap | UCSC genome browser: 14q24.1 | |
| Type of gene | protein-coding | |
| RefGenes | NM_152443.2, | |
| Description | all-trans and 9-cis retinol dehydrogenaseretinol dehydrogenase 12retinol dehydrogenase 12, all-trans and 9-cisshort chain dehydrogenase/reductase family 7C, member 2 | |
| Modification date | 20141219 | |
| dbXrefs | MIM : 608830 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000139988 | ||
| HPRD : 10585 | ||
| Vega : OTTHUMG00000170032 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_RDH12 | |
| BioGPS: 145226 | ||
| Pathway | NCI Pathway Interaction Database: RDH12 | |
| KEGG: RDH12 | ||
| REACTOME: RDH12 | ||
| Pathway Commons: RDH12 | ||
| Context | iHOP: RDH12 | |
| ligand binding site mutation search in PubMed: RDH12 | ||
| UCL Cancer Institute: RDH12 | ||
| Assigned class in TissGDB* | C | |
| Included tissue-specific gene expression resources | TiGER,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. |
| Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
| GO ID | GO term | PubMed ID | GO:0042572 | retinol metabolic process | 12226107 | GO:0042572 | retinol metabolic process | 12226107 |
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| TissGeneExp for RDH12 |
| 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) |
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| 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) |
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| 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. |
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| 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) |
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| - Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
| Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
| THCA | 1.222408982 | 2.820229321 | -1.597820339 | 1.64E-09 | 9.19E-09 |
| KIRC | 1.259833276 | 2.997184665 | -1.737351389 | 1.57E-05 | 3.62E-05 |
| LUSC | 0.476103864 | -0.992274567 | 1.468378431 | 8.25E-06 | 1.89E-05 |
| KIRP | 0.297344734 | 3.827457234 | -3.5301125 | 2.01E-08 | 1.45E-07 |
| HNSC | 3.1459294 | 4.952775912 | -1.806846512 | 0.00568 | 0.015070755 |
| COAD | -0.418998775 | -1.442537237 | 1.023538462 | 0.000202 | 0.000681945 |
| KICH | -0.300549391 | 2.399834609 | -2.700384 | 5.87E-05 | 0.000160914 |
| STAD | 1.098666609 | 4.038760359 | -2.94009375 | 8.57E-06 | 0.000100911 |
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| TissGene-miRNA for RDH12 |
| 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 type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
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| TissGeneMut for RDH12 |
| TissGeneSNV for RDH12 |
| 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. |
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| 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) |
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| - nsSNVs sorted by frequency. |
| AAchange | Cancer type | # samples |
| p.D187N | SKCM | 2 |
| p.A60T | PRAD | 1 |
| p.R314Q | UCEC | 1 |
| p.S10F | LUSC | 1 |
| p.S190I | LUAD | 1 |
| p.K88N | READ | 1 |
| p.D187N | COAD | 1 |
| p.L153I | LUAD | 1 |
| p.E54K | SKCM | 1 |
| p.G46D | HNSC | 1 |
| p.R193H | STAD | 1 |
| p.R57S | LUSC | 1 |
| p.G50S | STAD | 1 |
| p.G39A | LUAD | 1 |
| p.G29E | SKCM | 1 |
| p.T299R | BLCA | 1 |
| p.F25L | UCEC | 1 |
| p.H148Q | KIRP | 1 |
| p.M130T | BRCA | 1 |
| p.D101N | READ | 1 |
| p.E110K | KIRP | 1 |
| p.G145R | HNSC | 1 |
| p.R62Q | STAD | 1 |
| p.G52C | UCEC | 1 |
| p.R302C | UCEC | 1 |
| p.E82K | SKCM | 1 |
| p.S90C | BLCA | 1 |
| p.T49M | HNSC | 1 |
| p.C245S | CHOL | 1 |
| p.V228L | KIRP | 1 |
| p.L277V | HNSC | 1 |
| p.L154I | COAD | 1 |
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| TissGeneCNV for RDH12 |
| 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) |
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| TissGeneFusions for RDH12 |
| Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
| Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
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| TissGeneNet for RDH12 |
| 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 |
| 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. |
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| 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. |
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| 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. |
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| 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. |
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| TissGeneClin for RDH12 |
| TissGeneDrug for RDH12 |
| Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
| DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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| TissGeneDisease for RDH12 |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0339527 | Leber Congenital Amaurosis | 10 | BeFree,ORPHANET |
| umls:C0854723 | Retinal Dystrophies | 8 | BeFree,CTD_human |
| umls:C0035304 | Retinal Degeneration | 7 | BeFree,CTD_human |
| umls:C0035334 | Retinitis Pigmentosa | 6 | BeFree,CLINVAR,CTD_human,GAD,LHGDN,ORPHANET |
| umls:C2675186 | LEBER CONGENITAL AMAUROSIS 13 | 6 | CLINVAR,CTD_human,UNIPROT |
| umls:C0035309 | Retinal Diseases | 5 | BeFree,GAD |
| umls:C0456909 | Blind Vision | 3 | GAD,LHGDN |
| umls:C0020490 | Hyperopia | 1 | BeFree |
| umls:C0311338 | Fundus Albipunctatus | 1 | BeFree |
| umls:C0339525 | Autosomal dominant retinitis pigmentosa | 1 | BeFree |
| umls:C0917796 | Optic Atrophy, Hereditary, Leber | 1 | GAD |
| umls:C1301509 | Severe visual impairment | 1 | BeFree |
| umls:C1858677 | LEBER CONGENITAL AMAUROSIS 3 (disorder) | 0 | CTD_human |
| umls:C3150208 | RETINITIS PIGMENTOSA 53 | 0 | CLINVAR |
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