Unsupervised hierarchical clustering based on our 2188-gene signature applied to external data sets.

<p>a) Clustering based on GSE4554 and b) Clustering based on the four largest batches of the TCGA RNAseqv2 data sets. MMR proficient tumors (green), microsatellite-low tumors (blue) and MMR deficient tumors (red) along the x-axis.</p

Clinical characteristics of the colorectal cancer subsets.

<p>Clinical characteristics of the colorectal cancer subsets.</p

qRT-PCR analysis of 5 target genes in the four different colorectal cancer subsets.

<p>Differential expression of <i>MYC, NDUFA9</i>, <i>H2AFZ</i>, <i>AXIN2</i>, and <i>DNA2</i> was done for 12 representative samples (3 from each group) and qRT-PCR ratios were normalized to rRNA18S and median centered.</p

Up-regulated signaling pathways in FCCTX and Lynch syndrome tumors.

<p>Up-regulated signaling pathways in FCCTX and Lynch syndrome tumors.</p

Additional file 1: of Identification of genetic variants for clinical management of familial colorectal tumors

Table S1. Primers used in the pCAS2 minigene splicing assay. (DOCX 15 kb

Clinicopathologic features of malignant and borderline ovarian tumors in the study cohort.

<p><i>Feature</i>: M = Malignant, Bo = Borderline; <i>Tissue type</i>: tissue used for RNA extraction, FT = Fallopian Tube, N/A = Unknown; <i>Survival</i>: Disease specific survival, Alive = alive at start of study; <i>C-signature</i>: corresponding ovarian molecular subtype <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107643#pone.0107643-Tothill1" target="_blank">[18]</a>; <i>BC subtype</i>: corresponding intrinsic breast cancer subtype <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107643#pone.0107643-Hu1" target="_blank">[22]</a>.</p><p>Clinicopathologic features of malignant and borderline ovarian tumors in the study cohort.</p

The 10 most significantly enriched biological processes in the malignant ovarian tumors in the study cohort [31].

<p>*FDR<0.05 and ≥3 recognized genes/biological function were required to consider a gene ontology (GO) process significant. 731 significant.</p><p>GO processes were identified.</p>a<p>Number of genes in the study cohort correlating to the GO process.</p>b<p>Number of genes in the GO process.</p><p>The 10 most significantly enriched biological processes in the malignant ovarian tumors in the study cohort <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107643#pone.0107643-Chen1" target="_blank">[31]</a>.</p

Intrinsic breast cancer subtypes.

<p>Serous ovarian tumors in the study cohort with corresponding intrinsic breast cancer subtypes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107643#pone.0107643-Hu1" target="_blank">[22]</a>. The rows outline the tumor types with the representation in each subtype in percent within parentheses. The p-value is calculated using Fisher's exact test.</p><p>Intrinsic breast cancer subtypes.</p

Ovarian cancer subtypes.

<p>Serous ovarian tumors in the study cohort with corresponding ovarian cancer subtypes (“C-signatures”) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107643#pone.0107643-Tothill1" target="_blank">[18]</a>. The rows outline the tumor types with the representation in each subtype in percent within parentheses. The p-value is calculated using Fisher's exact test.</p><p>Ovarian cancer subtypes.</p

Correlations between ovarian and breast cancer molecular subtypes.

<p>Correlations between specific ovarian cancer C-signatures <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107643#pone.0107643-Tothill1" target="_blank">[18]</a> and the intrinsic breast cancer subtypes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0107643#pone.0107643-Hu1" target="_blank">[22]</a> in the serous ovarian tumors in the study cohort. Tumors within each ovarian cancer C-signature are shown along the X axis, and the colored bars represent the percentage (on the Y axis) of each intrinsic breast cancer subtype within the respective C-signatures.</p