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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for NR2E3 |
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Phenotypic Information for NR2E3(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: NR2E3 |
Familial Cancer Database: NR2E3 |
* 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 | |
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145 |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: NR2E3 |
MedGen: NR2E3 (Human Medical Genetics with Condition) | |
ClinVar: NR2E3 | |
Phenotype | MGI: NR2E3 (International Mouse Phenotyping Consortium) |
PhenomicDB: NR2E3 |
Mutations for NR2E3 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NR2E3 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 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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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=13) | (# total SNVs=7) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr15:72106381-72106381 | p.H340H | 2 |
chr15:72104433-72104433 | p.M163T | 2 |
chr15:72106356-72106356 | p.T332M | 2 |
chr15:72103888-72103888 | p.Y62H | 1 |
chr15:72105733-72105733 | p.I251T | 1 |
chr15:72106440-72106440 | p.H360P | 1 |
chr15:72104149-72104149 | p.R97C | 1 |
chr15:72105743-72105743 | p.E254E | 1 |
chr15:72106454-72106454 | p.V365M | 1 |
chr15:72104306-72104306 | p.E121K | 1 |
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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 |   | 3 |   | 7 |   |   |   |   |   | 1 | 1 | 2 |   |   |   |   | 9 | 1 |   | 4 |
# mutation |   | 3 |   | 7 |   |   |   |   |   | 1 | 1 | 2 |   |   |   |   | 9 | 1 |   | 4 |
nonsynonymous SNV |   | 2 |   | 4 |   |   |   |   |   |   | 1 | 2 |   |   |   |   | 7 | 1 |   | 2 |
synonymous SNV |   | 1 |   | 3 |   |   |   |   |   | 1 |   |   |   |   |   |   | 2 |   |   | 2 |
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 |
chr15:72109942 | p.G369G | 2 |
chr15:72104776 | p.S224S,NR2E3 | 2 |
chr15:72105937 | p.E384Q | 2 |
chr15:72109899 | p.E319K,NR2E3 | 2 |
chr15:72104678 | p.S213P,NR2E3 | 1 |
chr15:72105876 | p.L378F | 1 |
chr15:72109951 | p.A383V | 1 |
chr15:72104690 | p.N237N,NR2E3 | 1 |
chr15:72105900 | p.L244L,NR2E3 | 1 |
chr15:72109971 | p.E387K | 1 |
Other DBs for Point Mutations |
Copy Number for NR2E3 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 NR2E3 |
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 |
AHSA2,ATG16L2,C20orf96,CATSPER3,DUSP28,GOLGA2P5,KIF12, L3MBTL1,LOC100131434,LOC100272228,LRRC37A3,MALAT1,NR2E3,PABPC1L, PRPF39,SUGT1P3,THSD4,TTC14,CFAP44,WFDC10A,ZMAT1 | ASB13,CA12,CCDC114,FGFR3,KIF12,LCN12,LRTOMT, MAPK15,MFSD6L,MTL5,NR2E3,NXNL2,PARD6B,PCP2, PPAPDC1B,PTPN1,SLC16A6,SLC1A2,SLC6A9,SMPD3,TMEM26 |
AFAP1L2,C15orf56,C6orf164,CDY2B,CELF6,CT62,GTF2A2, HPX,KLRAP1,LOC284009,NR2E3,OR1A2,OR2B2,PRB4, RGL3,RNF215,SAA1,SAA2,SEMG2,SYT12,TMCO5A | MROH7,DDX17,GK5,GOLGA8A,HERC2P2,LOC100131434,LOC91316, LRRC16B,MAMDC4,NR2E3,OTUD3,PDXDC2P,PILRB,PLXNB1, PRB1,PRR22,RBM6,RNF207,SEC31B,SIK1,YJEFN3 |
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 NR2E3 |
There's no related Drug. |
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Cross referenced IDs for NR2E3 |
* 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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