Gene ontology-enriched categories of synaptic mRNAs with least and most miRNA predicted interactions.

<p>GO-enriched categories determined by ClueGo in (<b>A</b>) transcripts with zero or one predicted miRNA site (<b>B</b>) transcripts with over eight different miRNA sites and (<b>C</b>) common to both transcript groups with least and most miRNA sites. A two-sided hypergeometric test yielded the enrichment for GO terms. Benjamini-Hochberg correction for multiple testing controlled the <i>P</i>-values.</p

Comparative analysis of shortest 3′UTR sequences from synaptic and non-synaptic control transcript groups.

<p>Boxplots depicting 3′UTR length of the electron-carrier activity, postsynaptic, presynaptic, ribosomal and rest protein-coding transcripts with the shortest 3′UTR sequence.</p

Comparative analysis of longest 3′UTR sequences from synaptic and non-synaptic control transcript groups.

<p>Boxplots depicting 3′UTR length of the electron-carrier activity, postsynaptic, presynaptic, ribosomal and rest protein-coding transcripts with the longest 3′UTR sequence.</p

Combination of weighted -lnp values of the three hexamers.

<p>The weight for hexamer 1 is on the Y axis, for hexamer 2 is held constant at a value of 1, and for hexamer 3 is on the X axis. The mean normalized difference of the correct miRNA versus the next highest miRNA was maximized for 5 datasets of knocked out miRNAs (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009171#s4" target="_blank">Methods</a>). The optimal weights combination for hexamers 1 and 3 were identified as 0.6 and 0 respectively. The value for hexamer 3 is still given in the Results page (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0009171#pone-0009171-g004" target="_blank">Figure 4</a>) although it is not used for the combined score calculation.</p

Schematic representation of the workflow.

<p>Schematic representation of the workflow.</p

Crossing scheme of the genome-wide insertional mutagenesis system.

<p>TREP 2.30 – promoter delivery, minimal promoter under tTA control, <i>w⁺</i> marker <i>CyO</i> [MiT 2.4] – <i>Minos</i> transposase source, CyO marker <i>Sco</i> – Sco marker BOEtTA – tTA source, <i>egfp</i> marker.</p

miRNA binding site density in synaptic 3′UTRs.

<p>Median values (interquartile range) of the binding site densities in the 3′UTR region of presynaptic, postsynaptic and rest protein-coding transcripts. All pairs with statistically significant differences are provided. IQR, interquartile range.</p

Interaction map between miRNAs and predicted pre- and post- synaptic mRNA targets.

<p>A set of ten miRNAs regulated 77% and 80% of pre- and post- synaptic transcripts, respectively. A script was used to identify the combination of miRNAs that were found to interact with the maximum number of synaptic mRNAs. Direct interactions between miRNAs and mRNAs are depicted with grey lines.</p

Results Page and links (Epithelial Ovarian Cancer).

<p>Genes upregulated and miRNAs downregulated in late stage Epithelial Ovarian Cancer (EOC) compared to early stage EOC were run through DIANA-mirExTra. The main results page (A) consists of two parts. At the top of the page is the histogram of the distribution of –lnp values for all possible hexamers and at the bottom, the sorted list of hexamers that can be mapped on deregulated miRNAs with corresponding p-values. The same hexamer can be shown multiple times if it can be mapped on more than one miRNAs. Hexamers are sorted according to p-value and negative natural logarithm (-lnp value). Following the link “View Results per microRNA” the user is taken to a page (B) showing miRNAs sorted according to a combinatorial score produced by the values of hexamers 1 and 2. The link “View Results per microRNA based on DIANA-microT target prediction scores” leads to a similar results page (C) that uses as a measure the scores of each gene according to miRNA target prediction program DIANA-microT. (D) Genes that contain at least one of the top ten hexamers are marked in the results page of DIANA-microT. The DIANA-microT results page for each miRNA can be found following the link on the miRNA name from the first results page. Additionally, links to DIANA-mirPath lead to a page (E) showing functional analysis results using this program. Genes containing the hexamer of interest (A), or targeted by the miRNA of interest (C) are mapped on KEGG pathways and the most significantly overrepresented pathways can be identified by their corresponding p-values.</p

A miRNA molecule binds to a miRNA target gene (miTG).

<p>Hexamers 1,2 and 3 correspond to six nucleotide long sequences on the 3′UTR complementary to the first nucleotides of the miRNA . Hexamer 2 is the sequence complementary to the ‘seed’ of the miRNA, which has been suggested as the most important region for miRNA:miTG binding.</p