The top 30 upregulated and downregulated genes in CEA+ and CEA- cells.

<p>The red color indicates upregulated mRNA; the blue color indicates downregulated mRNA. On the right side of the square are the names of the genes that differ in the expression between MIP101 (CEA-) and MIP101 clone 8 (CEA +) cell lines. The experiments were performed in two replicates starting from RNA extraction. As a control, we performed an analysis of the <i>CEA</i> gene and its isoforms expression level in these cell lines by RNA-seq data. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161256#pone.0161256.g002" target="_blank">Fig 2</a> shows plots of the <i>CEA</i> expression. Expression of the <i>CEA</i> gene is present in the CEA-producing line (MIP101 clone 8) and absent in the CEA-deficient cell line (MIP101). Moreover, CEA gene was represented by one isoform <i>CEACAM5-001</i> (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0161256#pone.0161256.g002" target="_blank">Fig 2B</a>).</p

Differential expression analysis results for <i>CEA (CEACAM5)</i> gene.

<p>a. Expression plot shows differences in the <i>CEACAM5</i> expression level between MIP101 (CEA-, blue color) and MIP101 clone 8 (CEA+, brown color) cell lines, measured in FPKM. Each sample was represented by two replicates. b. Expression level of <i>CEACAM5</i> is represented by single <i>CEACAM5-001</i> isoform.</p

Validation of RNA-Seq results was performed by qRT-PCR analysis on 5 randomly chosen genes from the list of differentially expressed genes.

<p>CEACAM5 also was analysed as positive control. Results obtained by RNA-Seq and qRT-PCR methods show high accordance. Each qRT-PCR was performed with three replicates. All data are means ± SD. (*p < 0.05; **p < 0.01, ***p < 0.001, one-way ANOVA for qRT-PCR and FDR-adjusted exact test for RNA-Seq).</p