Pairs of target sites for the same and different microRNAs.

<p>Proportion of pairs of target sites (y-axis) at a given distance (x-axis) for the same microRNAs (solid black line) and for two different microRNAs (dashed gray line).</p

Multiple uses of seedVicious.

<p>A) Cumulative distribution of the number of transcripts with at least two target sites with respect to the minimum distance between pairs of targets. The graph compares the distribution of all transcript (black), transcript/microRNA pairs with experimentally validated interactions (blue) and those with strongly validated interactions (red) according to miRTarBase. B) Precision of microRNA target prediction for different cut-offs of minimum distance between pairs of targets. The peak corresponds to a distance of 6, that is, two contiguous target sites. C) Precision of microRNA target prediction for multiple targets sites for the same microRNA. D) Evolutionary turnover of microRNA canonical target sites for let-7 in lin-14 in roundworm species using maximum parsimony.</p

Distance between canonical target sites.

<p>Distance between canonical target sites as defined by seedVicious (A), and the partial overlap of targets that are 6 nucleotides away (B).</p

MicroRNA target and near-target sites.

<p>Canonical and marginal sites are described in Bartel, 2009 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195532#pone.0195532.ref001" target="_blank">1</a>]. Near-target sites can be defined for all type of sites. The figure also shows that each seed (sixmer) 18 possible near-target sites as defined by Marco, 2015 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195532#pone.0195532.ref006" target="_blank">6</a>].</p

A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification-1

<p><b>Copyright information:</b></p><p>Taken from "A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification"</p><p>http://www.biomedcentral.com/1471-2105/8/442</p><p>BMC Bioinformatics 2007;8():442-442.</p><p>Published online 15 Nov 2007</p><p>PMCID:PMC2213689.</p><p></p>nces while the one on the right serves to show more clearly the underlying topology

A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification-0

<p><b>Copyright information:</b></p><p>Taken from "A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification"</p><p>http://www.biomedcentral.com/1471-2105/8/442</p><p>BMC Bioinformatics 2007;8():442-442.</p><p>Published online 15 Nov 2007</p><p>PMCID:PMC2213689.</p><p></p>mulative hypergeometric values are ranked to obtain rank-specific random distributions of the value. Although it is not indicated in the figure, results for each rank are obtained from independent sets of simulations

A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification-2

<p><b>Copyright information:</b></p><p>Taken from "A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification"</p><p>http://www.biomedcentral.com/1471-2105/8/442</p><p>BMC Bioinformatics 2007;8():442-442.</p><p>Published online 15 Nov 2007</p><p>PMCID:PMC2213689.</p><p></p>mulative hypergeometric values are ranked to obtain rank-specific random distributions of the value. Although it is not indicated in the figure, results for each rank are obtained from independent sets of simulations

The origin of microRNAs of <i>Schistosoma mansoni</i>.

<p>A) MicroRNAs characterized from small RNA libraries and their evolutionary origin based on homology searches. B) Example of a newly discovered microRNA in <i>S. mansoni</i> that is also conserved in <i>S. japonicum</i>. Conserved nucleotides between the two species are shown with a black background. The number of uniquely mapped reads for each sequence in <i>S. mansoni</i> is shown in the right, for both SOLiD and MiSeq datasets.</p

Real-time PCR validation of sex-biased expressed microRNAs.

1<p>Log Fold Change for the differences between Ct values for target and control microRNAs.</p>2<p>P-values based on t-test of Ct value differences for three technical replicates.</p

Sex-biased expression of microRNAs in <i>S.</i><i>mansoni</i>.

<p>A) Smear plot of normalized expression levels (log fold-change) for microRNAs in male and female samples against the total read counts (log average count). Black line indicates equal expression in both sexes. Grey lines represent 2-fold changes between samples. Filled circles are microRNAs with a significant expression fold change between sexes (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0002402#s4" target="_blank">Materials and Methods</a>). B) Relative enrichment/paucity of sex-biased microRNAs in the sex chromosome (ZW). Each expression level fold-change threshold (x-axis) is plotted against the logarithm of the p-value (Fisher's exact test) for enrichment or paucity in the sex chromosome.</p