Insertion patterns of CIS gene families.

<p>For each of five families the columns indicate which tumors contained an insertion for that specific member of a family. Rows indicate specific tumors.</p

A network of significant co-occurring and mutually exclusive common insertion sites (CISs).

<p>CISs are indicated by their manually curated target gene. Red edges indicate a co-occurrence relationship, while green edges indicate a mutually exclusive relationship. The number in parenthesis and the size of the nodes indicate the number of tumors with a viral insertion in the relevant CIS. The thickness of the edges is a measure of the significance of the relationship between the nodes.</p

MMTV integrations in two novel CISs.

<p>The putative target gene is shown, with the arrow indicating the transcriptional direction. Arrowheads indicate the genomic location of the viral integrations, with the direction of the arrow indicating the viral transcription direction. Colors indicate the cohort from which the integrations were recovered.</p

Analysis of clonality between different families of genes.

<p><b>A.</b> A heatmap of all combinations of gene families and single genes not assigned to a family. Significant difference in clonality for each family are calculated using a binominal test for all samples that are co-inserted in that specific gene (family) pair. Blue squares indicate a significant clonal relation from the group indicated on the Y-axis to the group indicated on the X-axis. Yellow squares indicate a significant clonal relationship from the X-axis to the Y-axis. Black squares indicate no significant relation. <b>B.</b> A network view of the heatmap in A. showing only significant (P<0.05) clonality relationships. An edge points from the more clonal gene(family) to the lesser clonal gene(family). The thickness of an edge is a measure of the significance of the clonality relation. For the fraction displayed on the edges, the numerator represents the number of times the parent node had a higher clonality score while the denominator represents the number of times the child node had a higher clonality score, in a tumor that contained insertions in both nodes.</p

Significant known and novel common insertion sites.

<p>This table gives an overview of the significant CISs and their potential target genes.</p>1<p>Although Fgfr1 has not been found as a common insertion site in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0062113#pone.0062113-Theodorou1" target="_blank">[11]</a>, the authors do mention finding one insertion near the gene.</p>2<p>The <i>Myb</i> CIS is a merge of two overlapping CISs (upstream and downstream of the <i>Myb</i> gene).</p