Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for RPE65
Basic gene info.Gene symbolRPE65
Gene nameretinal pigment epithelium-specific protein 65kDa
SynonymsBCO3|LCA2|RP20|mRPE65|rd12|sRPE65
CytomapUCSC genome browser: 1p31
Genomic locationchr1 :68894506-68915642
Type of geneprotein-coding
RefGenesNM_000329.2,
Ensembl idENSG00000116745
DescriptionBCO family, member 3RBP-binding membrane proteinall-trans-retinyl-palmitate hydrolasep63retinal pigment epithelium-specific 65 kDa proteinretinitis pigmentosa 20 (autosomal recessive)retinoid isomerohydrolaseretinol isomerase
Modification date20141222
dbXrefs MIM : 180069
HGNC : HGNC
Ensembl : ENSG00000116745
HPRD : 01569
Vega : OTTHUMG00000009208
ProteinUniProt: Q16518
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPE65
BioGPS: 6121
Gene Expression Atlas: ENSG00000116745
The Human Protein Atlas: ENSG00000116745
PathwayNCI Pathway Interaction Database: RPE65
KEGG: RPE65
REACTOME: RPE65
ConsensusPathDB
Pathway Commons: RPE65
MetabolismMetaCyc: RPE65
HUMANCyc: RPE65
RegulationEnsembl's Regulation: ENSG00000116745
miRBase: chr1 :68,894,506-68,915,642
TargetScan: NM_000329
cisRED: ENSG00000116745
ContextiHOP: RPE65
cancer metabolism search in PubMed: RPE65
UCL Cancer Institute: RPE65
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of RPE65 in cancer cell metabolism1. 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)
check002.gifCancer Description
Cancer CGAP: RPE65
Familial Cancer Database: RPE65
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
KEGG_RETINOL_METABOLISM

check002.gifOthers
OMIM 180069; gene.
204100; phenotype.
613794; phenotype.
Orphanet 180; Choroideremia.
364055; Severe early-childhood-onset retinal dystrophy.
65; Leber congenital amaurosis.
791; Retinitis pigmentosa.
DiseaseKEGG Disease: RPE65
MedGen: RPE65 (Human Medical Genetics with Condition)
ClinVar: RPE65
PhenotypeMGI: 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryRPE65chr16891224868912268AGBL4chr14910166549101685
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPE65 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI480708CLIC611263213608999136090243RPE6526365516889467668895066

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=13

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=72)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=3)
Stat. for Insertions
(# total SNVs=1)

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr1:68904763-68904763p.V287D13
chr1:68905294-68905294p.I225I3
chr1:68910517-68910517p.V99I2
chr1:68904634-68904634p.C330F2
chr1:68906582-68906582p.N199K2
chr1:68904865-68904865p.?2
chr1:68904681-68904681p.H314H2
chr1:68896760-68896760p.E480K2
chr1:68910558-68910558p.R85H2
chr1:68903931-68903931p.N356fs*172

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 192 2 4  1332 1163 8
# mutation 1 182 2 4  1432 1193 11
nonsynonymous SNV 1 122 1 2  1232 1122 6
synonymous SNV   6  1 2  2    71 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr1:68905294p.I225I3
chr1:68910558p.G140W2
chr1:68910291p.R124L2
chr1:68910338p.H314H2
chr1:68904681p.V99I2
chr1:68910517p.R85H2
chr1:68897259p.A514T1
chr1:68910232p.T400I1
chr1:68910529p.R296R1
chr1:68904697p.D167D1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

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
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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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

: Open all cross reference information



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