SylArray: a web server for automated detection of miRNA effects from expression data.
A useful step for understanding the function of microRNAs (miRNA) or siRNAs is the detection of their effects on genome-wide expression profiles. Typically, approaches look for enrichment of words in the 3(')UTR sequences of the most deregulated genes. A number of tools are available for this purpose, but they require either in-depth computational knowledge, filtered 3(')UTR sequences for the genome of interest, or a set of genes acquired through an arbitrary expression cutoff. To this end, we have developed SylArray; a web-based resource designed for the analysis of large-scale expression datasets. It simply requires the user to submit a sorted list of genes from an expression experiment. SylArray utilizes curated sets of 3(')UTRs to attach sequences to these genes and then applies the Sylamer algorithm for detection of miRNA or siRNA signatures in those sequences. An intuitive system for visualization and interpretation of the small RNA signatures is included.


BACKGROUND
SylArray is written in Perl-CGI, Perl and Java and also uses the R statistical package. The source-code, database and web resource are freely available under GNU Public License (GPL). The web server is freely accessible at http://www.ebi.ac.uk/enright/sylarray.
Bartonicek
Nenad
N
EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
Enright
Anton J
AJ
D020413:3' Untranslated Regions; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D016678:Genome; D023281:Genomics / Q000379:methods*; D035683:MicroRNAs / Q000235:genetics*; D012313:RNA / Q000235:genetics; D012984:Software; D014584:User-Computer Interface
D020413:3' Untranslated Regions; D035683:MicroRNAs; D012313:RNA