Fraction of reads mapped vs. number of reads in the quality trimmed <i>Homo sapiens</i> RNA-Seq dataset.

<p>Each symbol corresponds to a quality threshold. Peak Q parameters for each tool are reported.</p

Barplots indicating the performance of nine read trimming tools at different quality thresholds on a <i>Homo sapiens</i> RNA-Seq dataset.

<p>For ConDeTri, two basic parameters are necessary, and combinations of both are reported (which explains the non-monotonic appearance of the barplots). Red bars indicate the percentage of reads aligning in the trimmed dataset. Blue bars indicate the number of reads surviving trimming.</p

Comparative assessment of variant detection based on <i>Prunus persica</i> reads aligned on the reference peach genome.

<p>Several read trimming method/threshold combinations are tested. The Average Percentage of Minor Allele Call (APOMAC) or of Non-reference Allele Call (APONAC) are reported, together with the total number of high-confidence SNPs.</p

Number of covered nucleotides in the <i>Prunus persica</i> genome (total size: 227M bases) above minimum coverage thresholds.

<p>The analysis was performed on untrimmed reads and after trimming with 9 tools at Q=20 (for ConDeTri, default parameters HQ=25 and LQ=10 were used).</p

Computational requirements necessary for full <i>Prunus persica</i> genome assembly (RAM peak and time) for different combinations of read trimming tools and thresholds.

<p>Computational requirements necessary for full <i>Prunus persica</i> genome assembly (RAM peak and time) for different combinations of read trimming tools and thresholds.</p

Example of novel prediction by CINDy.

<p>Proposed mechanism for modulation of HMGA1 by CDK2.</p

Schematic representations of the CINDy algorithm.

<p>A collection of gene expression profiles is required to calculate Conditional Mutual Information between lists of modulators, transcription factors and putative target genes, with the final output of inferred modulation events.</p

Alternative three-way network topologies including a Transcription Factor (TF), a Target gene (Tg) and a Modulator gene (M).

<p>(A) depicts the independent regulation of the target gene by a modulator and a TF; (B) describes a three-way interaction between the TF, the target gene and the modulator.</p

Comparative performance of MINDy and CINDy.

<p>Precision and recall values are compared in the B-cell lymphoma dataset (panel A) and Lung Adenocarcinoma dataset (panel B), calculated by matching the predictions with a gold standard dataset set obtained from four different databases of experimentally validated PPIs between modulators and transcription factors. Precision and recall are further compared at different robustness threshold for MINDy (blue line) and CINDy (red line) in the B-cell dataset (panel C) and in the Lung dataset (panel D, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109569#s4" target="_blank"><b>Materials and Methods</b></a>).</p

Default parameters used for running MINDy.

<p>NA: Not applicable.</p><p>Default parameters used for running MINDy.</p