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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RDH11 |
Basic gene info. | Gene symbol | RDH11 |
Gene name | retinol dehydrogenase 11 (all-trans/9-cis/11-cis) | |
Synonyms | ARSDR1|CGI82|HCBP12|MDT1|PSDR1|RALR1|RDJCSS|SCALD|SDR7C1 | |
Cytomap | UCSC genome browser: 14q24.1 | |
Genomic location | chr14 :68143518-68162510 | |
Type of gene | protein-coding | |
RefGenes | NM_001252650.1, NM_016026.3, | |
Ensembl id | ENSG00000072042 | |
Description | HCV core-binding protein HCBP12androgen-regulated short-chain dehydrogenase/reductase 1prostate short-chain dehydrogenase reductase 1prostate short-chain dehydrogenase/reductase 1retinal reductase 1retinol dehydrogenase 11short chain dehydrogenase/r | |
Modification date | 20141207 | |
dbXrefs | MIM : 607849 | |
HGNC : HGNC | ||
Ensembl : ENSG00000072042 | ||
HPRD : 09707 | ||
Vega : OTTHUMG00000171196 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RDH11 | |
BioGPS: 51109 | ||
Gene Expression Atlas: ENSG00000072042 | ||
The Human Protein Atlas: ENSG00000072042 | ||
Pathway | NCI Pathway Interaction Database: RDH11 | |
KEGG: RDH11 | ||
REACTOME: RDH11 | ||
ConsensusPathDB | ||
Pathway Commons: RDH11 | ||
Metabolism | MetaCyc: RDH11 | |
HUMANCyc: RDH11 | ||
Regulation | Ensembl's Regulation: ENSG00000072042 | |
miRBase: chr14 :68,143,518-68,162,510 | ||
TargetScan: NM_001252650 | ||
cisRED: ENSG00000072042 | ||
Context | iHOP: RDH11 | |
cancer metabolism search in PubMed: RDH11 | ||
UCL Cancer Institute: RDH11 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for RDH11(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: RDH11 |
Familial Cancer Database: RDH11 |
* 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 REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: RDH11 |
MedGen: RDH11 (Human Medical Genetics with Condition) | |
ClinVar: RDH11 | |
Phenotype | MGI: RDH11 (International Mouse Phenotyping Consortium) |
PhenomicDB: RDH11 |
Mutations for RDH11 |
* 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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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
pancreas | RDH11 | chr14 | 68149265 | 68149285 | RDH11 | chr14 | 68149357 | 68149377 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RDH11 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 |
AI928382 | CYCS | 4 | 298 | 7 | 25162451 | 25162745 | RDH11 | 298 | 443 | 14 | 68144286 | 68144431 | |
BM552700 | EPOR | 1 | 188 | 19 | 11491701 | 11491888 | RDH11 | 183 | 709 | 14 | 68156928 | 68159703 | |
BQ962146 | E2F1 | 32 | 154 | 20 | 32274048 | 32274170 | RDH11 | 151 | 749 | 14 | 68156930 | 68159775 | |
AI928208 | CYCS | 4 | 298 | 7 | 25162451 | 25162745 | RDH11 | 298 | 443 | 14 | 68144286 | 68144431 | |
AA658025 | KLK2 | 25 | 124 | 19 | 51382393 | 51382492 | RDH11 | 120 | 231 | 14 | 68143994 | 68144105 | |
BF432108 | RDH11 | 1 | 433 | 14 | 68143674 | 68144529 | PRSS23 | 425 | 550 | 11 | 86662375 | 86662500 | |
AI160852 | HNRNPH3 | 9 | 274 | 10 | 70101762 | 70102028 | RDH11 | 259 | 467 | 14 | 68145082 | 68151881 | |
BC017787 | RDH11 | 1 | 303 | 14 | 68159262 | 68162481 | IPO7 | 288 | 784 | 11 | 9467536 | 9468032 |
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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=22) | (# total SNVs=6) |
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(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr14:68151905-68151905 | p.T227T | 2 |
chr14:68157059-68157059 | p.L178L | 2 |
chr14:68159182-68159182 | p.R108* | 2 |
chr14:68162384-68162384 | p.L13M | 1 |
chr14:68151878-68151878 | p.Q236Q | 1 |
chr14:68159192-68159192 | p.T104T | 1 |
chr14:68162412-68162412 | p.E3D | 1 |
chr14:68159246-68159246 | p.Q86Q | 1 |
chr14:68145068-68145068 | p.S309S | 1 |
chr14:68156953-68156953 | p.Q214* | 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 | 1 | 1 |   | 3 |   |   | 1 |   | 4 | 1 |   | 2 |   | 1 | 1 |   | 3 | 5 |   | 1 |
# mutation | 1 | 1 |   | 3 |   |   | 1 |   | 4 | 1 |   | 2 |   | 1 | 1 |   | 3 | 5 |   | 1 |
nonsynonymous SNV |   | 1 |   | 2 |   |   | 1 |   | 3 |   |   | 2 |   | 1 |   |   | 1 | 1 |   | 1 |
synonymous SNV | 1 |   |   | 1 |   |   |   |   | 1 | 1 |   |   |   |   | 1 |   | 2 | 4 |   |   |
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 |
chr14:68157923 | p.Y202Y | 1 |
chr14:68151872 | p.G192G | 1 |
chr14:68159192 | p.L178L | 1 |
chr14:68151874 | p.F154F | 1 |
chr14:68159246 | p.P134R,RDH11 | 1 |
chr14:68151878 | p.S239S,RDH11 | 1 |
chr14:68159652 | p.V130M,RDH11 | 1 |
chr14:68151905 | p.H218N,RDH11 | 1 |
chr14:68159684 | p.T104T,RDH11 | 1 |
chr14:68156954 | p.D216E,RDH11 | 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 RDH11 |
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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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ATP6V1D,C14orf1,C14orf169,CALM1,CNIH1,COX16,EIF2B2, EIF2S1,ERH,EXD2,MTHFD1,AP5M1,PSEN1,PSMA3, RDH11,SLC39A9,SNAR-F,TMED10,VTI1B,WDR89,ZNF410 | AP1M2,C14orf1,VWA9,EFHD1,ETNK2,GOLM1,MYCBP, PDIA3,PDIA3P1,PPAPDC2,IFT22,RASL11B,RDH11,SEC14L2, SNRNP40,SPA17,STT3A,TCTN1,TCTN3,TM9SF1,XBP1 | ||||
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DNAAF2,C14orf1,C14orf166,DLST,EIF2B2,EIF2S1,ERH, EXD2,GLRX5,GNPNAT1,L2HGDH,MGAT2,MTHFD1,AP5M1, OXA1L,LRR1,PPP2R5E,RDH11,SCFD1,SLC39A9,TMEM135 | ARL13B,ARNTL2,C14orf1,C6orf223,CTPS1,DNAJC10,FDPS, HAUS6,HSD11B1,HSD17B7,IFITM3,NBN,NUCB2,OSMR, PLA2G2A,PLA2G3,RDH11,RTP1,S100A11,SC5D,STARD4 |
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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 RDH11 |
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DB Category | DB Name | DB's ID and Url link |
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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 |
DB00162 | retinol dehydrogenase 11 (all-trans/9-cis/11-cis) | approved; nutraceutical | Vitamin A | ![]() | ![]() |
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Cross referenced IDs for RDH11 |
* 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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