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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RDH5 |
Basic gene info. | Gene symbol | RDH5 |
Gene name | retinol dehydrogenase 5 (11-cis/9-cis) | |
Synonyms | 9cRDH|HSD17B9|RDH1|SDR9C5 | |
Cytomap | UCSC genome browser: 12q13-q14 | |
Genomic location | chr12 :56114150-56118526 | |
Type of gene | protein-coding | |
RefGenes | NM_001199771.1, NM_002905.3, | |
Ensembl id | ENSG00000135437 | |
Description | 11-cis RDH11-cis RoDH11-cis retinol dehydrogenase9-cis retinol dehydrogenase9-cis-retinol specific dehydrogenaseretinol dehydrogenase 1retinol dehydrogenase 5 (11-cis and 9-cis)short chain dehydrogenase/reductase family 9C, member 5 | |
Modification date | 20141207 | |
dbXrefs | MIM : 601617 | |
HGNC : HGNC | ||
Ensembl : ENSG00000135437 | ||
HPRD : 03370 | ||
Vega : OTTHUMG00000170126 | ||
Protein | UniProt: Q92781 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RDH5 | |
BioGPS: 5959 | ||
Gene Expression Atlas: ENSG00000135437 | ||
The Human Protein Atlas: ENSG00000135437 | ||
Pathway | NCI Pathway Interaction Database: RDH5 | |
KEGG: RDH5 | ||
REACTOME: RDH5 | ||
ConsensusPathDB | ||
Pathway Commons: RDH5 | ||
Metabolism | MetaCyc: RDH5 | |
HUMANCyc: RDH5 | ||
Regulation | Ensembl's Regulation: ENSG00000135437 | |
miRBase: chr12 :56,114,150-56,118,526 | ||
TargetScan: NM_001199771 | ||
cisRED: ENSG00000135437 | ||
Context | iHOP: RDH5 | |
cancer metabolism search in PubMed: RDH5 | ||
UCL Cancer Institute: RDH5 | ||
Assigned class in ccmGDB | B - This gene belongs to cancer gene. |
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Phenotypic Information for RDH5(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: RDH5 |
Familial Cancer Database: RDH5 |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
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KEGG_RETINOL_METABOLISM |
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OMIM | 136880; phenotype. 601617; gene. |
Orphanet | 227796; Fundus albipunctatus. 52427; Retinitis punctata albescens. |
Disease | KEGG Disease: RDH5 |
MedGen: RDH5 (Human Medical Genetics with Condition) | |
ClinVar: RDH5 | |
Phenotype | MGI: RDH5 (International Mouse Phenotyping Consortium) |
PhenomicDB: RDH5 |
Mutations for RDH5 |
* 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. |
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There's no structural variation information in COSMIC data for this gene. |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RDH5 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
AK309464 | CPT1A | 1 | 1887 | 11 | 68540732 | 68607152 | RDH5 | 1885 | 2165 | 12 | 56117668 | 56118220 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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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Stat. for Non-Synonymous SNVs (# total SNVs=13) | (# total SNVs=17) |
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(# total SNVs=1) | (# total SNVs=1) |
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* 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 position | Mutation(aa) | Unique sampleID count |
chr12:56117724-56117724 | p.F208L | 2 |
chr12:56115156-56115156 | p.S63Y | 2 |
chr12:56115654-56115654 | p.V164V | 2 |
chr12:56115687-56115687 | p.Y175Y | 1 |
chr12:56118152-56118152 | p.D260D | 1 |
chr12:56115191-56115191 | p.R75C | 1 |
chr12:56117671-56117671 | p.R191W | 1 |
chr12:56115013-56115013 | p.L15L | 1 |
chr12:56118164-56118164 | p.V264V | 1 |
chr12:56115258-56115258 | p.E97G | 1 |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   | 3 | 1 | 1 |   |   |   |   | 2 | 3 |   | 1 | 2 | 1 |   |   | 1 | 3 |   | 5 |
# mutation |   | 3 | 1 | 1 |   |   |   |   | 2 | 3 |   | 1 | 2 | 1 |   |   | 1 | 3 |   | 5 |
nonsynonymous SNV |   | 1 | 1 |   |   |   |   |   | 1 | 2 |   | 1 | 1 | 1 |   |   | 1 | 2 |   | 2 |
synonymous SNV |   | 2 |   | 1 |   |   |   |   | 1 | 1 |   |   | 1 |   |   |   |   | 1 |   | 3 |
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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* 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 Position | Mutation(aa) | Unique sampleID count |
chr12:56115654 | p.V164V,RDH5 | 2 |
chr12:56118203 | p.F208F,RDH5 | 1 |
chr12:56118266 | p.E216K,RDH5 | 1 |
chr12:56115013 | p.L15L,RDH5 | 1 |
chr12:56117671 | p.E219Q,RDH5 | 1 |
chr12:56118299 | p.R19G,RDH5 | 1 |
chr12:56115023 | p.R251C,RDH5 | 1 |
chr12:56117672 | p.R21P,RDH5 | 1 |
chr12:56115030 | p.V264V,RDH5 | 1 |
chr12:56117674 | p.S23S,RDH5 | 1 |
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* 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. |
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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 RDH5 |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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ADIPOQ,AOC3,AQP7,AQP7P1,C14orf180,CIDEC,FABP4, GLYAT,GPD1,GPR146,GPX3,HEPACAM,HEPN1,ITIH5, KCNIP2,LEP,LIPE,NPR1,PLIN1,PLIN4,RDH5 | ACO1,AIFM2,ALDH2,AOC3,AQP7,BTD,FAM213A, CALB2,CIDEC,EHD2,GPD1,HEPN1,LIPE,PLIN1, RDH5,RETSAT,TFE3,TK2,TYRO3,VEGFB,VTI1B | ||||
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ACADS,AKR1B15,AQP7,BBOX1,BCO1,TMEM253,EXOC3L4, CIDEC,GAL3ST1,LIMA1,LOC100130933,METTL7B,MS4A8,MYO1A, P2RX4,POLD4,RDH5,RETSAT,SULT1A2,TM6SF2,VILL | ACADS,ACSF2,B3GNT8,CMBL,COQ4,ECHS1,ESPN, FAM73B,HTATIP2,LPCAT3,MAP2K2,METTL7B,NR1H3,PHGR1, RDH5,SLC27A4,SPHK2,TMEM120A,TMEM139,TPRG1L,ZFYVE19 |
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* 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 |
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Pharmacological Information for RDH5 |
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DB Category | DB Name | DB's ID and Url link |
Organism-specific databases | PharmGKB | PA34308; -. |
Organism-specific databases | CTD | 5959; -. |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00157 | retinol dehydrogenase 5 (11-cis/9-cis) | approved; nutraceutical | NADH | ![]() | ![]() |
DB00162 | retinol dehydrogenase 5 (11-cis/9-cis) | approved; nutraceutical | Vitamin A | ![]() | ![]() |
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Cross referenced IDs for RDH5 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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