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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for RAE1 |
Basic gene info. | Gene symbol | RAE1 |
Gene name | ribonucleic acid export 1 | |
Synonyms | MIG14|MRNP41|Mnrp41|dJ481F12.3|dJ800J21.1 | |
Cytomap | UCSC genome browser: 20q13.31 | |
Genomic location | chr20 :55926617-55953519 | |
Type of gene | protein-coding | |
RefGenes | NM_001015885.1, NM_003610.3, | |
Ensembl id | ENSG00000101146 | |
Description | RAE1 RNA export 1 homologhomolog of yeast Rae1 (Bharathi) mRNA-associated protein of 41 kDa (Kraemer)mRNA export factormRNA export proteinmRNA-associated protein MRNP 41mRNA-binding protein, 41-kDmigration-inducing gene 14rae1 protein homolog | |
Modification date | 20141207 | |
dbXrefs | MIM : 603343 | |
HGNC : HGNC | ||
HPRD : 11939 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_RAE1 | |
BioGPS: 8480 | ||
Gene Expression Atlas: ENSG00000101146 | ||
The Human Protein Atlas: ENSG00000101146 | ||
Pathway | NCI Pathway Interaction Database: RAE1 | |
KEGG: RAE1 | ||
REACTOME: RAE1 | ||
ConsensusPathDB | ||
Pathway Commons: RAE1 | ||
Metabolism | MetaCyc: RAE1 | |
HUMANCyc: RAE1 | ||
Regulation | Ensembl's Regulation: ENSG00000101146 | |
miRBase: chr20 :55,926,617-55,953,519 | ||
TargetScan: NM_001015885 | ||
cisRED: ENSG00000101146 | ||
Context | iHOP: RAE1 | |
cancer metabolism search in PubMed: RAE1 | ||
UCL Cancer Institute: RAE1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for RAE1(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: RAE1 |
Familial Cancer Database: RAE1 |
* 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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REACTOME_METABOLISM_OF_NON_CODING_RNA REACTOME_METABOLISM_OF_RNA REACTOME_METABOLISM_OF_CARBOHYDRATES |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: RAE1 |
MedGen: RAE1 (Human Medical Genetics with Condition) | |
ClinVar: RAE1 | |
Phenotype | MGI: RAE1 (International Mouse Phenotyping Consortium) |
PhenomicDB: RAE1 |
Mutations for RAE1 |
* 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 RAE1 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 |
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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 | 2 |   |   |   |   |   | 1 |   |   |   |   |   |   |   | 1 |   |   | |||
GAIN (# sample) | 2 |   |   |   |   |   | 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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Stat. for Non-Synonymous SNVs (# total SNVs=30) | (# total SNVs=5) |
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(# total SNVs=4) | (# 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 |
chr20:55948626-55948626 | p.P248fs*29 | 3 |
chr20:55948793-55948793 | p.A275V | 3 |
chr20:55949675-55949675 | p.A280T | 2 |
chr20:55940493-55940493 | p.A124T | 2 |
chr20:55942062-55942062 | p.? | 2 |
chr20:55929173-55929173 | p.N27D | 1 |
chr20:55948631-55948631 | p.P248L | 1 |
chr20:55940431-55940431 | p.T103M | 1 |
chr20:55953129-55953129 | p.E361K | 1 |
chr20:55943782-55943782 | p.A186P | 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 | 4 | 4 |   | 3 |   |   |   |   |   |   |   | 2 | 3 | 1 |   | 2 | 3 | 4 |   | 11 |
# mutation | 4 | 4 |   | 3 |   |   |   |   |   |   |   | 3 | 3 | 1 |   | 2 | 3 | 4 |   | 12 |
nonsynonymous SNV | 4 | 4 |   | 3 |   |   |   |   |   |   |   | 2 | 2 | 1 |   | 2 | 1 | 3 |   | 10 |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   | 1 | 1 |   |   |   | 2 | 1 |   | 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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* 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 |
chr20:55949675 | p.A124T,RAE1 | 2 |
chr20:55940493 | p.A275V,RAE1 | 2 |
chr20:55948535 | p.A280T,RAE1 | 2 |
chr20:55948793 | p.R216L,RAE1 | 2 |
chr20:55940431 | p.N254D,RAE1 | 1 |
chr20:55953148 | p.C143Y,RAE1 | 1 |
chr20:55948583 | p.A275S,RAE1 | 1 |
chr20:55940437 | p.S148S,RAE1 | 1 |
chr20:55948590 | p.R159L,RAE1 | 1 |
chr20:55949710 | p.A275A,RAE1 | 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 RAE1 |
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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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AURKA,GID8,RTFDC1,CSE1L,CSTF1,DDX27,LSM14B, PFDN4,PSMA7,RAB22A,RAE1,RBM38,SLMO2,SS18L1, STAU1,STX16,TAF4,NELFCD,TPD52L2,VAPB,YTHDF1 | ABCB9,GID8,RHPN1-AS1,FAM110A,FAM83H,GPR143,KLHL35, MAPK8IP2,OSBP2,PGAP2,PRMT5,PTDSS1,PVT1,RAE1, RFC5,ST6GALNAC2,NELFCD,TRIB3,UMPS,ZNF16,ZNF7 |
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ATP5E,GID8,AAR2,RTFDC1,CSE1L,CSTF1,DPM1, EIF2S2,MOCS3,PDRG1,PSMA7,RAE1,RNF114,SLMO2, NELFCD,TP53RK,TPD52L2,UBE2V1,UQCC1,VAPB,YTHDF1 | CCDC138,CDCA4,COPZ1,EED,FBXO5,GTPBP10,IMMP1L, MRPL3,NHP2L1,NPM1,NR2C2AP,NUP35,NUP37,ORC5, PCNA,POLR2G,PRMT5,RAD51AP1,RAE1,RPL17,SNRPD3 |
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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 RAE1 |
There's no related Drug. |
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Cross referenced IDs for RAE1 |
* 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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