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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RPE65 |
Basic gene info. | Gene symbol | RPE65 |
Gene name | retinal pigment epithelium-specific protein 65kDa | |
Synonyms | BCO3|LCA2|RP20|mRPE65|rd12|sRPE65 | |
Cytomap | UCSC genome browser: 1p31 | |
Genomic location | chr1 :68894506-68915642 | |
Type of gene | protein-coding | |
RefGenes | NM_000329.2, | |
Ensembl id | ENSG00000116745 | |
Description | BCO family, member 3RBP-binding membrane proteinall-trans-retinyl-palmitate hydrolasep63retinal pigment epithelium-specific 65 kDa proteinretinitis pigmentosa 20 (autosomal recessive)retinoid isomerohydrolaseretinol isomerase | |
Modification date | 20141222 | |
dbXrefs | MIM : 180069 | |
HGNC : HGNC | ||
Ensembl : ENSG00000116745 | ||
HPRD : 01569 | ||
Vega : OTTHUMG00000009208 | ||
Protein | UniProt: Q16518 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RPE65 | |
BioGPS: 6121 | ||
Gene Expression Atlas: ENSG00000116745 | ||
The Human Protein Atlas: ENSG00000116745 | ||
Pathway | NCI Pathway Interaction Database: RPE65 | |
KEGG: RPE65 | ||
REACTOME: RPE65 | ||
ConsensusPathDB | ||
Pathway Commons: RPE65 | ||
Metabolism | MetaCyc: RPE65 | |
HUMANCyc: RPE65 | ||
Regulation | Ensembl's Regulation: ENSG00000116745 | |
miRBase: chr1 :68,894,506-68,915,642 | ||
TargetScan: NM_000329 | ||
cisRED: ENSG00000116745 | ||
Context | iHOP: RPE65 | |
cancer metabolism search in PubMed: RPE65 | ||
UCL Cancer Institute: RPE65 | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of RPE65 in cancer cell metabolism | 1. Amann PM, Luo C, Owen RW, Hofmann C, Freudenberger M, et al. (2012) Vitamin A metabolism in benign and malignant melanocytic skin cells: importance of lecithin/retinol acyltransferase and RPE65. Journal of cellular physiology 227: 718-728. go to article |
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Phenotypic Information for RPE65(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: RPE65 |
Familial Cancer Database: RPE65 |
* 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/ |
Metabolic Pathway Description | |
KEGG_RETINOL_METABOLISM |
Others | |
OMIM | 180069; gene. 204100; phenotype. 613794; phenotype. |
Orphanet | 180; Choroideremia. 364055; Severe early-childhood-onset retinal dystrophy. 65; Leber congenital amaurosis. 791; Retinitis pigmentosa. |
Disease | KEGG Disease: RPE65 |
MedGen: RPE65 (Human Medical Genetics with Condition) | |
ClinVar: RPE65 | |
Phenotype | MGI: RPE65 (International Mouse Phenotyping Consortium) |
PhenomicDB: RPE65 |
Mutations for RPE65 |
* 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | RPE65 | chr1 | 68912248 | 68912268 | AGBL4 | chr1 | 49101665 | 49101685 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPE65 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 |
BI480708 | CLIC6 | 11 | 263 | 21 | 36089991 | 36090243 | RPE65 | 263 | 655 | 1 | 68894676 | 68895066 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   | |||
GAIN (# sample) |   | 1 |   |   |   |   |   |   |   |   |   |   |   |   | 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=72) | (# total SNVs=20) |
(# total SNVs=3) | (# total SNVs=1) |
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Top 10 SNVs Having the Most Samples in COSMIC data |
* 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 |
chr1:68904763-68904763 | p.V287D | 13 |
chr1:68905294-68905294 | p.I225I | 3 |
chr1:68914341-68914341 | p.E20E | 2 |
chr1:68906565-68906565 | p.N205S | 2 |
chr1:68910517-68910517 | p.V99I | 2 |
chr1:68904634-68904634 | p.C330F | 2 |
chr1:68906582-68906582 | p.N199K | 2 |
chr1:68904865-68904865 | p.? | 2 |
chr1:68904681-68904681 | p.H314H | 2 |
chr1:68896760-68896760 | p.E480K | 2 |
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SNV Counts per Each Loci in TCGA data |
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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 |   | 19 | 2 |   | 2 |   | 4 |   |   | 13 | 3 | 2 |   | 1 | 16 | 3 |   | 8 |
# mutation |   | 1 |   | 18 | 2 |   | 2 |   | 4 |   |   | 14 | 3 | 2 |   | 1 | 19 | 3 |   | 11 |
nonsynonymous SNV |   | 1 |   | 12 | 2 |   | 1 |   | 2 |   |   | 12 | 3 | 2 |   | 1 | 12 | 2 |   | 6 |
synonymous SNV |   |   |   | 6 |   |   | 1 |   | 2 |   |   | 2 |   |   |   |   | 7 | 1 |   | 5 |
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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Top 10 SNVs Having the Most Samples in TCGA data |
* 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 |
chr1:68905294 | p.I225I | 3 |
chr1:68910517 | p.R124L | 2 |
chr1:68910558 | p.H314H | 2 |
chr1:68910291 | p.V99I | 2 |
chr1:68910338 | p.R85H | 2 |
chr1:68904681 | p.G140W | 2 |
chr1:68905261 | p.D483D | 1 |
chr1:68912489 | p.R347H | 1 |
chr1:68895600 | p.L133I | 1 |
chr1:68897198 | p.R44Q | 1 |
Other DBs for Point Mutations |
Copy Number for RPE65 in TCGA |
* 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. |
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 RPE65 |
Gene Expression in Cancer Cell-lines (CCLE) |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
Differential Gene Expression in Primary Tumors (TCGA) |
* 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-Expressed gene's network Plot |
* 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 |
A2M,ACTG2,BTBD18,CECR7,CSPG4,HAPLN3,KCNMB1, LCTL,LGR6,LOC100190939,MYLK,PRKX,RASL12,ROPN1, RPE65,SERPINB11,SRSF12,SHC4,SNX22,SOX10,TAGLN | BCL2L14,BDNF,TYMSOS,CABYR,CDH4,CPXCR1,GLRA2, IL1RL2,LOC121838,MMP3,NPPC,OBP2B,OTOF,RPE65, SH3GL3,SHANK1,SLC7A5P1,SNORA5B,TAS2R1,UGT8,ULBP3 |
AMPD1,ARSF,BATF3,CDKN2B-AS1,FAM135B,HLA-DMA,HLA-DOA, HLA-DRB6,HS3ST1,IFIT1B,KYNU,RNF152,RPE65,SAA1, SAA2,SAA4,SCARA5,SGK1,TYMP,VAMP5,VAT1L | AARSD1,BAG3,C1orf194,LINC00472,DCLK2,DLGAP1,EFHC2, FST,GPR20,HSPA4L,KLF8,MARK1,METTL8,MMP16, MYADM,NLGN4Y,PLXNB3,RPE65,SIX2,TRPC6,UBE2G2 |
Co-Expressed gene's Protein-protein interaction Network Plot |
* 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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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for RPE65 |
There's no related Drug. |
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Cross referenced IDs for RPE65 |
* 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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