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

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

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

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

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

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