Example of novel prediction by CINDy.

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

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

Default parameters used for running MINDy.

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

Reference mutations of myeloid malignancy.

(DOCX)</p

Detection of the Challenging mutations at 1% VAF and 50 ng DNA input.

Detection of the Challenging mutations at 1% VAF and 50 ng DNA input.</p

Schematic overview of the cross-platform study.

Reference samples: Sample set one or set two tested at 30 ng or 50 ng (per vendor’s protocol specification, Table 1) and 10 ng input respectively. For each input level, four samples carrying mutations at VAF of 0%, 0.125%, 0.5% and 1% respectively were tested in duplicate.</p

Coverage of reference gene panel by assay A to E for reference samples.

Coverage of reference gene panel by assay A to E for reference samples.</p

Assay specifications from the vendors.

Assay specifications from the vendors.</p