Volcano plot with the correlation between the GI50 values for Cisplatin (A&C) and Paclitaxel (B&D) and the expression of each mRNA (A&B) or microRNA (C&D).

<p><i>X-axes spearman correlation, Y-axes -Log of the p-value.</i></p

Hierarchical clustering based on the expression of the 1141 genes and 18 microRNAs differentially expressed between the three morphological subtypes.

<p><i>Histology & Putative Histology</i>: S serous, HGS high-grade serous, LGS low-grade serous, E endometrioid, C clear cell, Mx mixed, M mucinous, <i>Morphology</i>: E Epithelial, R Round, S Spindle, <i>Red colour</i> high expression, <i>Green colour</i> low expression.</p

Hierarchical clustering of 26 cell lines and 267 ovarian carcinomas based on the expression of the 1141 morphological subtypes-associated genes (A) and the association with progression-free survival (B).

<p>The diseases and functions associated with gene clusters A-D are shown together with the p-value and the number of genes associated (#). <i>Red colour</i> high expression, <i>Green colour</i> low expression.</p

Overview of the cell line characteristics.

<p><i>Morphology</i>: E Epithelial, R Round, S Spindle, <i>Histology & Putative Histology</i>: S serous, HGS high-grade serous, LGS low-grade serous, E endometrioid, C clear cell, Mx mixed, M mucinous. <i>Origin</i>: A ascites, T tumour tissue, TM tissue from metastasis, TO ovarian tumour tissue, P pleural effusion. <i>Time</i>: P primary disease, R relapsed disease, CR at clinical resistance. <i>Platinum treated</i>: U untreated, P platinum-based treatment, O other chemotherapy, R radiotherapy. <i>Protein markers</i>: bright red no expression (signal –to-noise ratio <5), light red low expression (signal –to-noise ratio 5–20), light green expression (signal –to-noise ratio 20–200), bright green high expression (signal –to-noise ratio >200), grey not determined. <i>Therapy response</i>: green to red scale sensitive to resistant. <i>Doubling time</i>: green less than one day, yellow 1–2days, orange >2days. <i>MSI</i> microsatellite instability. <i>Gene mutations</i>: dark blue identified by at least two methods, light blue identified by one method, light red identified with one method BUT not with second method. <i>Gene amplification</i>: orange amplified (2–3x SD above the median), red highly amplified (>3x SD above the median). The WNT/bCatenin pathway (WNT/bCAT) and homologous recombination repair (HRR) columns show the number of mutated genes in these pathways.</p

Association of chemotherapy response (concentration causing 50% growth-inhibition) with doubling time (T2, hours) and protein marker expression (s/n) in 33 unique ovarian cancer cell lines.

<p>T2 doubling time, LumCK luminal cytokeratins, Spearman correlation and (p-value) are shown in bold when significant (p<0.05).</p><p>Association of chemotherapy response (concentration causing 50% growth-inhibition) with doubling time (T2, hours) and protein marker expression (s/n) in 33 unique ovarian cancer cell lines.</p

Overview of the presented data, results and <i>in silico</i> clinical translation.

<p><i>STR short tandem repeat, MSI microsatellite instability, PFS progression-free survival</i>.</p

Patient characteristics, clinicopathologic features and the molecular subtypes defined by Tothill et al. relative to the morphological clusters.

§<p>Pearson Chi-square test,</p>¥<p>Fisher's Exact,</p>£<p>Two-sample Wilcoxon rank-sum (Mann-Whitney) test.</p><p>Patient characteristics, clinicopathologic features and the molecular subtypes defined by Tothill et al. relative to the morphological clusters.</p

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

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