Distribution of selected mutations along the different affected genes and their related functional categories.

<p>A) Number of mutated samples by gene according to the described mutation filtering protocol (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0148346#pone.0148346.s002" target="_blank">S2 Fig</a>). Only 33 recurrent genes were included. B) Number of mutated samples by gene category (bottom). The corresponding number of genes included in each functional category (top) is also represented in order to avoid any size bias. C) The functional categories are distributed depending on the observed mutated samples and the known number of belonging genes. Both transcription factor and ubiquitination categories shown and excess of mutated samples. D) The number of mutated samples per category in the haloplex cohort were compared against a reference population of healthy samples (1000 genomes). Here, while metabolism and signalling genes categories appear poorly mutated, ubiquitination appears remarkably more mutated than the reference population.</p

Mutated genes with a higher frequency in our cohort than expected in the 1000 genomes repository.

<p>Mutated genes with a higher frequency in our cohort than expected in the 1000 genomes repository.</p

Network of significant gene co-occurrences.

<p>Genes are represented by nodes and their sizes defined from the number of significant co-occurrences they are implied. Edges represent co-occurrences between pairs of genes. Every edge is labelled with the number of samples that carries the mutated pair of genes as follows: higher than expected co-occurrences are coloured in green, while lower than expected (only one) in red. Edge width is proportional to the statistical p-value of chi-square test. Those genes co-occurring only at one single patient are painted in white. Seven co-occurrence subnetworks arise from the significant co-occurrence network, where remarkably a single component connected the half of represented genes. In contrast, 3 pairs are simultaneously mutated only in 2 different individuals, and 3 significant co-occurrence subnetworks, only in 1 patient.</p

Network-based analysis (SNOW) applied to 46 selected genes (33 recurrent and <i>RARA</i>, <i>PML</i>, and <i>FLT3</i> genes).

<p>The network was complemented with the co-occurrence relationships, in order to summarize the two kind of significant results. Significant network-based analysis genes are coloured in light blue and stroked with a magenta border whether they resulted also significant in co-occurrence analysis. Genes only included by co-occurrence are coloured in magenta. Intermediate genes were painted in white and square shaped. While grey edges represent protein-protein interaction, relationships, broad orange dashed lines describe significant co-occurrences. Moreover, main genes are grouped depending on their biological role (cohesin complex, signalling pathways, spliceosome, RHO-GTPase, retinoic acid regulators and other cellular processes roles).</p

SNV and indel filtering steps for identification of somatic variants.

<p>SNV and indel filtering steps for identification of somatic variants.</p