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Protocols

EnsMart specifications

Information


Unique identifier OMICS_25437
Name EnsMart
Restrictions to use None
Database management system MySQL
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

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Publication for EnsMart

EnsMart citations

 (17)
call_split

IL2RG, identified as overexpressed by RNA seq profiling of pancreatic intraepithelial neoplasia, mediates pancreatic cancer growth

2017
Oncotarget
PMCID: 5663522
PMID: 29137350
DOI: 10.18632/oncotarget.19848
call_split See protocol

[…] were identified using the program AltAnalyze. AltAnalyze ( www.altanalyze.org) was run on BED files for RNA-sequencing data from 12 samples: three normal pancreatic duct and nine PanIN-3 samples. The EnsMart65 database was used as a reference. The ASPIRE algorithm, described in detail in the AltAnalyze manual ( http://www.altanalyze.org/help_main.htm), was used to score exon inclusion/exclusion ev […]

library_books

Ubiquitination of the spliceosome auxiliary factor hnRNPA1 by TRAF6 links chronic innate immune signaling with hematopoietic defects and myelodysplasia

2016
Nat Immunol
PMCID: 5423405
PMID: 28024152
DOI: 10.1038/ni.3654

[…] uences were retrieved using R/Bioconductor’s (http://www.bioconductor.org) BSgenome packages. All exons and flanking introns (with explicit start-end coordinates) defined in TXdb (for SpliceTrap) and EnsMart65 (for AltAnalyze) were used as search spaces to compute the total occurrence and location of each predicted binding site (see below). Entire exon blocks (merged Ensembl transcript models from […]

library_books

Astrocytic CCAAT/Enhancer Binding Protein Delta Contributes to Glial Scar Formation and Impairs Functional Recovery After Spinal Cord Injury

2015
Mol Neurobiol
PMCID: 5085997
PMID: 26510742
DOI: 10.1007/s12035-015-9486-6

[…] nt in primary cultures of wild-type astrocytes compared with those in C/EBPδ −/− astrocytes (Fig. ). Moreover, after three putative C/EBP binding motifs were identified (Fig. , upper panel) using the EnsMart System (www.ensembl.org/biomart/martview/c6c926d9815de045873590a6da1ac151), our reporter assay demonstrated that the activity of the MMP-3 reporter rose significantly after IL-1β treatment in […]

library_books

RFX transcription factors are essential for hearing in mice

2015
Nat Commun
PMCID: 4634137
PMID: 26469318
DOI: 10.1038/ncomms9549

[…] ysed data set was used as the background set. The promoter regions examined spanned from 1,000 nt upstream to 500 nt downstream the TSS. Mouse, human and zebrafish orthologous genes were mapped using ENSMART utility. In all tests of HC-elevated genes, the top scoring motif matched the known binding signature of RFX TFs. The location distribution of this motif consistently showed a very sharp peak […]

library_books

Cellular Adhesion Gene SELP Is Associated with Rheumatoid Arthritis and Displays Differential Allelic Expression

2014
PLoS One
PMCID: 4141704
PMID: 25147926
DOI: 10.1371/journal.pone.0103872

[…] ed. SNPs with previously published disease associations or known functional consequences (e.g. non-synonymous coding SNPs) if existent were preferred. Information on SNPs was retrieved from databases EnsMart (http://www.ensembl.org/), PupaSNP , UCSC (http://genome.ucsc.edu), HapMap (www.hapmap.org), and dbSNP (http://www.ncbi.nlm.nih.gov/SNP/). […]

library_books

Effect of Duplicate Genes on Mouse Genetic Robustness: An Update

2014
Biomed Res Int
PMCID: 4119742
PMID: 25110693
DOI: 10.1155/2014/758672

[…] the number of nonsynonymous substitutions per nonsynonymous site (d N) between mouse and human orthologs were estimated by the maximum likelihood method using PAML [] and were retrieved from Ensembl EnsMart. For mouse genes have many human (rat) orthologs, the pair with the smallest d N/d S ratio was used for further analysis.We calculated the protein connectivity (k) based on the protein-protein […]

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EnsMart institution(s)
European Bioinformatics Institute (EBI), Hinxton, Cambridge, UK; The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
EnsMart funding source(s)
Supported mainly by the Wellcome Trust with additional funding from EMBL, and by the ArrayExpress project from the European Commission (TEMBLOR/DESPRAD).

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