GI classes have different position in PPI-network.

<p><b>(a)</b> Physical interaction degree of gene products in the protein-protein interaction (PPI) network (only genes coding for proteins with at least one interacting partner were considered). *<i>P</i> < 10⁻³, Wilcoxon rank-sum test, indicates significant difference when compared to GIs-all and other GI classes. <b>(b)</b> Enrichment of PPI-Hubs in GI classes when compared to GIs-all. -Log₁₀ of <i>P-values</i> obtained using Fisher’s tests are indicated. The area over the red dashed line indicates significant enrichment (<i>P</i> < 0.05). <b>(c)</b> Illustration of bottlenecks and the different type of nodes in the protein-protein interaction (PPI) network (adapted from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004738#pcbi.1004738.ref036" target="_blank">36</a>]). <b>(d-e)</b> Betweenness centrality of non-Hub and Hub gene products. *<i>P</i> < 10⁻³, Wilcoxon rank-sum test, indicates significant difference when compared to other GI classes. The box plots (a, d-e) represent the min, max, 25^th, 50^th (median) and 75^th percentile of either PPI Degree (k) or betweenness centrality values.</p

GI classes are enriched in within-pathways interactions.

<p><b>(a)</b> Schematic representation of possible relationships between genetic interactions (GIs) and pathways. Each node represents a gene being part of pathways 1 or 2. A red line indicates a within-pathway GI and a blue line, a between-pathway GI. <b>(b-c)</b> Log-Ratio scores for within-pathway (red bars) and between-pathway (blue bars) relationships observed between genes interacting through different GI classes, or present in GIs-all. A positive Log-Ratio score means that the frequency of within- or between-pathways GIs occurring in the GI class is significantly higher than the frequency of similar situations witnessed in relevant randomized GI networks with a probability of 0.99 (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004738#sec017" target="_blank">Methods</a>).</p

GI classes have different functions.

<p><b>(a)</b> Summary of Gene Ontology (GO) term enrichments for interacting genes in individual genetic interactions (GIs) classes when compared to interacting genes from GIs-all. Only the statistically significant enrichments are shown with adjusted <i>P</i>-values. An asterisk (*) means that the GI class is also enriched with the functional annotation when gene repetitions were not considered (<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004738#pcbi.1004738.s023" target="_blank">S2 Table</a>). <b>(b)</b> Enrichments of essential gene sets (Kamath et al. and Soninchsen et al. taken from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004738#pcbi.1004738.ref028" target="_blank">28</a>] and [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004738#pcbi.1004738.ref029" target="_blank">29</a>]) in GI classes when compared to GIs-all. <b>(c)</b> Enrichment of redundant and evolutionarily conserved genes in GI classes when compared to GIs-all. The redundant gene list was made of 306 genes taken from [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004738#pcbi.1004738.ref030" target="_blank">30</a>]. (b-c) -Log₁₀ of <i>P-</i>values obtained using Fisher’s exact tests are indicated. The area over the red dashed line indicates significant enrichment (<i>P</i> < 0.05).</p

Identifying GI classes.

<p><b>(a)</b> Positive (GIs, black lines) and negative (Random gene pairs, white lines) examples of genetic interactions were clustered based on their attribute scores using unsupervised methods. Columns show values for the six attributes used to predict interactions in [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004738#pcbi.1004738.ref054" target="_blank">54</a>]. Each individual attribute is either a measure of genes co-expression levels (<i>Exp</i>) or enrichment of shared phenotypes (<i>Ph</i>). They are also indicator for whether the neighborhoods of the genes of interest are enriched with the same phenotype (<i>N</i>). Here we define the neighborhood of a given gene as the set of genes that show significant co-expression with it (<i>P</i> ≤ 0.05, see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004738#sec017" target="_blank">Methods</a>) and/or encode proteins that exhibit a PPI with the product of this gene. <i>NPh</i> is an indicator like <i>N</i> with the additional requirement that the genes of interest themselves must also exhibit the phenotype enriched in their neighborhoods. Attributes <i>I and CI</i> indicate that interacting genes code for interacting proteins or for proteins sharing a significantly high number of common protein-protein interaction partners. Scores correspond to the following valuation: 1 or 0 (on a binary system) for <i>N</i>, <i>NPh</i> and <i>I</i> attributes. (1 –(<i>P</i>-value <0.05)) for <i>Exp</i>, <i>Ph</i> and <i>CI</i> attributes. <b>(b)</b> Positive examples of genetic interactions were clustered and identified by the color code on the left.</p

GI classes define PDS-depend and -independent modules.

<p><b>(a)</b> Schematic representation of possible relationships between genetic interactions (GIs) and protein-protein dense subnetworks (PDS). Each node represents a gene being part of PDS1 or PDS2. A red line indicates a within-PDS GI and a blue line, a between-PDS GI. <b>(b)</b> Log-Ratio scores for within-PDS (red bars) and between-PDS (blue bars) relationships observed between genes interacting through different GI classes, or present in GIs-all. A positive Log-Ratio score means that the frequency of within- or between-PDS GIs occurring in the GI class is significantly higher than the frequency of similar situations witnessed in relevant randomized GI networks with a probability of 0.99 (see <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004738#sec017" target="_blank">Methods</a>).</p

Defining pleiotropic and non-pleiotropic connectors.

<p><b>(a)</b> Box plots showing distributions of genetic interaction (GI) degrees for GIs-all and the six classes of GIs. Distributions were found to be significantly higher (Dark grey boxes) or lower (white boxes) than GIs-all (<i>P</i> < 0.05, Wilcoxon rank-sum test). Light grey boxes indicate classes with GI degree not significantly different than GIs-all. <b>(b)</b> Enrichment in GI-Hubs (defined as the 20% most connected genes in GIs-all) for GI classes when compared to GIs-all. <b>(c)</b> Distribution of pleiotropic indices (PIs) for GIs-all and the six classes of GIs. Dark grey, white and light grey boxes are designated as in panel (a). <b>(d)</b> Enrichment in High-PI (defined as the top 20% of genes with the highest PIs genome-wide) for GI classes when compared to GIs-all. The box plots (a, c) represent the min, max, 25^th, 50^th (median) and 75^th percentile of either GI Degree (a) or pleiotropic indices (c). (b, d) -Log₁₀ of <i>P</i>-values obtained using Fisher’s tests are indicated. The area over the red dashed line indicates significant enrichment (<i>P</i> < 0.05).</p

Data integration is required to identify GI classes.

<p>Hierarchical clustering of <b>(a)</b> Enrichment in GI classes and GI groups of Genetic interaction-Hubs (GI-Hubs), redundant genes, protein-protein interaction-Hubs (PPI-Hubs), Highly pleiotropic genes (High-PI) and essential genes -log of P-values from Fisher’s exact test are indicated. GI groups are associated to a positive value (+; above a threshold) or a negative value (-; below the threshold) for indicated attributes. Threshold values for each attributes are indicated <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1004738#pcbi.1004738.s027" target="_blank">S6 Table</a>. <b>(b)</b> Log-Ratios profiles for GI classes and GI groups associated to a positive (+) or a negative (-) values for indicated attributes. Blue boxes indicate enrichment of biological characteristics for C4 and C5 GI classes and CI(+) GI group.</p

Association of Childhood Chronic Physical Aggression with a DNA Methylation Signature in Adult Human T Cells

<div><p>Background</p><p>Chronic physical aggression (CPA) is characterized by frequent use of physical aggression from early childhood to adolescence. Observed in approximately 5% of males, CPA is associated with early childhood adverse environments and long-term negative consequences. Alterations in DNA methylation, a covalent modification of DNA that regulates genome function, have been associated with early childhood adversity.</p><p>Aims</p><p>To test the hypothesis that a trajectory of chronic physical aggression during childhood is associated with a distinct DNA methylation profile during adulthood.</p><p>Methods</p><p>We analyzed genome-wide promoter DNA methylation profiles of T cells from two groups of adult males assessed annually for frequency of physical aggression between 6 and 15 years of age: a group with CPA and a control group. Methylation profiles covering the promoter regions of 20 000 genes and 400 microRNAs were generated using MeDIP followed by hybridization to microarrays.</p><p>Results</p><p>In total, 448 distinct gene promoters were differentially methylated in CPA. Functionally, many of these genes have previously been shown to play a role in aggression and were enriched in biological pathways affected by behavior. Their locations in the genome tended to form clusters spanning millions of bases in the genome.</p><p>Conclusions</p><p>This study provides evidence of clustered and genome-wide variation in promoter DNA methylation in young adults that associates with a history of chronic physical aggression from 6 to 15 years of age. However, longitudinal studies of methylation during early childhood will be necessary to determine if and how this methylation variation in T cells DNA plays a role in early development of chronic physical aggression.</p></div

DNA Methylation Signature of Childhood Chronic Physical Aggression in T Cells of Both Men and Women

<div><p>Background</p><p>High frequency of physical aggression is the central feature of severe conduct disorder and is associated with a wide range of social, mental and physical health problems. We have previously tested the hypothesis that differential DNA methylation signatures in peripheral T cells are associated with a chronic aggression trajectory in males. Despite the fact that sex differences appear to play a pivotal role in determining the development, magnitude and frequency of aggression, most of previous studies focused on males, so little is known about female chronic physical aggression. We therefore tested here whether or not there is a signature of physical aggression in female DNA methylation and, if there is, how it relates to the signature observed in males.</p><p>Methodology/Principal Findings</p><p>Methylation profiles were created using the method of methylated DNA immunoprecipitation (MeDIP) followed by microarray hybridization and statistical and bioinformatic analyses on T cell DNA obtained from adult women who were found to be on a chronic physical aggression trajectory (CPA) between 6 and 12 years of age compared to women who followed a normal physical aggression trajectory. We confirmed the existence of a well-defined, genome-wide signature of DNA methylation associated with chronic physical aggression in the peripheral T cells of adult females that includes many of the genes similarly associated with physical aggression in the same cell types of adult males.</p><p>Conclusions</p><p>This study in a small number of women presents preliminary evidence for a genome-wide variation in promoter DNA methylation that associates with CPA in women that warrant larger studies for further verification. A significant proportion of these associations were previously observed in men with CPA supporting the hypothesis that the epigenetic signature of early life aggression in females is composed of a component specific to females and another common to both males and females.</p></div

Gene promoters differentially methylated between women CPA (n = 5) and NPA (n = 14) in T cells.

<p><b>A</b>. Numbers of promoters with significant methylation increases and decreases in CPA versus NPA (P<0.05; FDR<0.05). <b>B.</b> Heatmap depicts normalized intensities of microarray probes contained in promoters that best differentiate between CPA and NPA groups. Probes were selected from gene promoters called differentially methylated with respect to aggression groups (P≤0.05; FDR ≤0.05). One probe was selected for each gene, always the probe with the most extreme t-statistic. Heatmaps are colored so the median values on each row are gray, high values are red and low values are green. Red indicates higher methylation in a row and green indicates lower methylation. Clustering was performed using Ward’s hierarchical clustering algorithm with Pearson correlation distance as the distance metric. Rows correspond to promoters and columns to subjects.</p