Pol II density profiles of Fos and Jun in resting and activated B cells.

<p>Pol II density profiles in the genomic region along (a) Fos and (b) Jun genes in RESTB and ACTB cells. Data were normalized as reads per million reads mapped (TPM).</p

Biological processes enriched in poised with background of Pol II⁺ genes.

<p>Biological processes enriched in poised with background of Pol II⁺ genes.</p

Distributions of Pol II density and its poising index.

<p>Violin plots showing (a) the distributions of Pol II promoter density, (b) Pol II gene body density, and (c) poising index values for 9710 genes in ACTB and 9290 genes in RESTB cells with Pol II⁺ promoters. Pol II densities were normalized to reads per kilobase per million reads mapped (RPKM). The y-axes are in a logarithmic scale.</p

Biological processes enriched in non-poised genes with background of Pol II⁺ genes.

<p>Biological processes enriched in non-poised genes with background of Pol II⁺ genes.</p

Changes in Pol II profile, gene expression, and poising index upon B cell activation.

<p>a) Violin plots comparing distributions of fold changes of Pol II promoter density (left) and Pol II gene body density (right) for two groups genes: genes that continued to be poised after B cell activation (6802 genes) and genes that switch from poised to non-poised class during B cell activation (1138 genes). The y-axes are in a logarithmic scale. The p-values from Mann Whitney U test and Cohen's d effect sizes that reflect the differences between two groups are reported on top. b) Violin plots comparing the distributions of fold changes of poising index and mRNA expression in two groups of genes based on their change in transcriptional activity along gene body upon B cell activation: genes with similar Pol II body density (2/3 < fold change < 1.5; 6069 genes) and genes with large increase of Pol II body density (fold change > 1.5; 1491 genes) between RESTB and ACTB. c) The Spearman and partial Spearman correlations between changes in gene expression and changes in Pol II promoter/gene body density during the transition from RESTB to ACTB for common 8769 Pol II⁺ genes.</p

Biological processes enriched in poised genes with background of all genes.

<p>Biological processes enriched in poised genes with background of all genes.</p

mRNA expression of immediate early genes in resting B cells and calls activated for 30m, 3h, 24h, and 72h.

<p>Comparison of mRNA expression levels of all genes (a) in resting B cells and the cells activated for 30 minutes, (b) 30 minutes and 3 hours, (c) 3 hours and 24 hours, and (d) 24 hours and 72 hours. Six immediate early genes are highlighted. (e) Time series of expression levels of six immediate early genes.</p

The impact of B cell activation on Pol II profile.

<p>Nodes correspond to the Pol II profile classes. Arrows correspond to Pol II profile changes when transitioning from a given profile class in RESTB (arrow start) to a profile class in ACTB (arrow end). The labels along the arrows display the percentage of genes that change the profile class consistently with the arrow. The labels also include GO enrichment terms for the group of genes with the corresponding profile change. GO enrichment analyses were done with the background of all of Pol II⁺ promoter genes in either RESTB or ACTB.</p

Statistical differences in the number of G4 sequence motifs between poised and non-poised genes, and between high and low ratio of expression at 30m over 72h after cell activation.

<p>We plot p-values of the Mann-Whitney-Wilcoxon tests in log scale. The relative position of the bars with respect to the central line indicates enriched category for a given gene group.</p

Overview of three settings for which BeWith was applied.

<p>(A) The goal of BeME-WithFun is to discover modules which have dense functional interactions within the modules while having mutually exclusive mutations with genes in other modules (B) In BeME-WithCo we aim to identify modules which have co-occurring mutations within the modules while having mutual exclusivity between the modules (C) In BeCo-WithMEFun, we look for modules of functional and mutual exclusivity relations inside a module with co-occurring mutations between modules.</p