Sylarray

Sylarray detects enriched microRNA (miRNA) and small interfering RNA (siRNA) sequence signatures in genome-wide expression data by linking sorted gene lists to curated 3' untranslated region (3'UTR) sequences and testing for motif enrichment.

Key Features:

• Sorted gene list input: Accepts a sorted list of genes derived from expression experiments as the primary input for analysis.
• Curated 3'UTR sequences: Attaches curated sets of 3'UTR sequences to submitted genes to enable identification of potential small RNA target sites.
• Sylamer algorithm integration: Employs the Sylamer algorithm to detect enriched motifs indicative of miRNA or siRNA activity within 3'UTRs.
• Visualization outputs: Produces visualizations of detected small RNA signature enrichment for downstream interpretation.
• Open-source implementation: Implemented in Perl-CGI, Perl, Java, and the R statistical package and distributed under the GNU Public License (GPL).

Scientific Applications:

• Small RNA effect detection: Identifies miRNA and siRNA signatures in genome-wide expression profiles to study RNA-mediated regulation of gene expression.
• Gene regulation and biomarker discovery: Supports investigations into the roles of miRNAs and siRNAs in biological processes and disease and can aid identification of novel therapeutic targets or biomarkers.

Methodology:

Accepts a sorted gene list, attaches curated 3'UTR sequences to those genes, applies the Sylamer algorithm to detect enriched motifs within 3'UTRs, and outputs visualizations; implemented in Perl-CGI, Perl, Java, and R and distributed under the GNU Public License (GPL).