Hierarchical clustering and heat map with the 9 genes composing the signature discriminating ATC and PTC samples.

<p>Hierarchical clustering and heat map with the 9 genes composing the signature discriminating ATC and PTC samples.</p

Heat map for genes belonging to some significant Gene Ontology (GO) categories (p-Value <1) corresponding to several biological processes which illustrate the more malignant character of ATC compared to PTC.

<p>Heat map for genes belonging to some significant Gene Ontology (GO) categories (p-Value <1) corresponding to several biological processes which illustrate the more malignant character of ATC compared to PTC.</p

Additional file 1: of New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer

Figure S1 to S9 and Table S1 to S4. (PDF 1467 kb

Additional file 2: of New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer

Supplemental materials and methods. (PDF 652 kb

Venn diagrams of the significantly A) upregulated genes in all ATC and all PTC and B) downregulated genes in all ATC and all PTC.

<p>Venn diagrams of the significantly A) upregulated genes in all ATC and all PTC and B) downregulated genes in all ATC and all PTC.</p

Validation of the 9 genes signature by qRT-PCR on 5 new PTC and 5 new ATC.

<p>The microarray expressions is also represented. Log₂ ratios represent the expression ratios of the genes in the tumors versus a pool of 23 normal thyroid tissues.</p

Multidimensional scaling (MDS) of the mRNA expression data from 11 ATC and 48 PTC (all the probes present on the array were considered).

<p>The ATC are labelled according to their mutation as depicted in the figure.</p

Normalized luciferase activity in HEK293 cells cotransfected during 24 h or 48 h with the 3′UTR-LOX construction or with the mutated construction (3′UTR-LOX mutated: partial deletion of the seed sequence) and with miR-29a or with the scramble.

<p>The seed sequence is represented in blue and the * indicates a p-value<5%.</p

Heatmap based on the results of SAM one class analysis of the microarray data from 6 thyroid cancer cell lines and compared to tumor tissues.

<p>18 of the 19 modulated miRNA in cell lines are modulated in the same way in ATC, but are not modulated or in an opposite way in differentiated tumors (PTC and FTC). The heatmap was generated using R 2.14.1. with the library “gplots”. ATC.M (n = 11), PTC.M (n = 8) and FTC.M (n = 8) refer to the mean of the miRNA data from the different tumors analyzed. * miRNA described as regulated in ATC by Braun et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111581#pone.0111581-Braun1" target="_blank">[23]</a>. # miRNA described as regulated in ATC by Visone et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0111581#pone.0111581-Visone1" target="_blank">[24]</a>.</p

Proposed scheme synthetizing the miRNA and mRNA expression analyses of the same 11 ATC and highlighting the EMT feature of this tumor.

<p>Only direct binding of miRNA on mRNA are represented (green: downregulated m(i)RNA; red: upregulated m(i)RNA.</p