<p>There are 552 genes selected from the RNA-Seq data (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124523#pone.0124523.s018" target="_blank">S9 Table</a>) and 1030 unique genes selected from the microarray analysis (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124523#pone.0124523.s022" target="_blank">S13 Table</a>). Note that 146 unique genes are found from both platforms to be unequivocally expressed and altered by salt-loading (See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124523#pone.0124523.s023" target="_blank">S14</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0124523#pone.0124523.s024" target="_blank">S15</a> Tables)....
<p>Note the widespread transcriptional response of AECs to flagellin in monolayer cultures compared ...
<p>The diagram clearly depicted that only 5 DEGs shared between 20°C and 20°C plus Cu and 58 DEGs be...
<p>Three RNA samples from the FlpIn-3T3 control cell line, three samples from the FlpIn-3T3 Pax6(5a)...
<p>A: Venn diagram summarizing the overlap between differentially expressed genes from RNA-Seq (<i>l...
<p>(A) The average number of hits (log2(x+1)) for each gene are plotted on the y-axis and the corres...
<p>For final analyses we selected 9344 and 7494 genes for which sense transcripts were detected by S...
<p>Four lists of genes that were differentially expressed at least 1.5-fold between the indicated co...
<p>The venn diagram shows a summary of the log-fold changes of batch transcription data, which revea...
MOTIVATION: RNA-seq co-expression analysis is in its infancy and reasonable practices remain poorly ...
<p>Ecl8Δ<i>ramA</i> or Ecl8Δ<i>ramR</i> were used as calibrators in the pairwise comparisons. The ar...
Intersections of detected genes among tested pipelines. Genes with TPM >â0.1 were defined as being...
(a)-(d) use significant genes from the edgeR Exact, SAMSeq, EBSeq, DESeq2, and Voom methods; (e)—(h)...
<p><b>(A)</b> Venn diagram showing the number of common and unique genes, upregulated and downregula...
<p>(A) The fold-change values from the mRNA-seq data (x-axis) are plotted against the fold change va...
<p>Venn diagrams showing the intersection of significant genes differentially downregulated (A) and ...
<p>Note the widespread transcriptional response of AECs to flagellin in monolayer cultures compared ...
<p>The diagram clearly depicted that only 5 DEGs shared between 20°C and 20°C plus Cu and 58 DEGs be...
<p>Three RNA samples from the FlpIn-3T3 control cell line, three samples from the FlpIn-3T3 Pax6(5a)...
<p>A: Venn diagram summarizing the overlap between differentially expressed genes from RNA-Seq (<i>l...
<p>(A) The average number of hits (log2(x+1)) for each gene are plotted on the y-axis and the corres...
<p>For final analyses we selected 9344 and 7494 genes for which sense transcripts were detected by S...
<p>Four lists of genes that were differentially expressed at least 1.5-fold between the indicated co...
<p>The venn diagram shows a summary of the log-fold changes of batch transcription data, which revea...
MOTIVATION: RNA-seq co-expression analysis is in its infancy and reasonable practices remain poorly ...
<p>Ecl8Δ<i>ramA</i> or Ecl8Δ<i>ramR</i> were used as calibrators in the pairwise comparisons. The ar...
Intersections of detected genes among tested pipelines. Genes with TPM >â0.1 were defined as being...
(a)-(d) use significant genes from the edgeR Exact, SAMSeq, EBSeq, DESeq2, and Voom methods; (e)—(h)...
<p><b>(A)</b> Venn diagram showing the number of common and unique genes, upregulated and downregula...
<p>(A) The fold-change values from the mRNA-seq data (x-axis) are plotted against the fold change va...
<p>Venn diagrams showing the intersection of significant genes differentially downregulated (A) and ...
<p>Note the widespread transcriptional response of AECs to flagellin in monolayer cultures compared ...
<p>The diagram clearly depicted that only 5 DEGs shared between 20°C and 20°C plus Cu and 58 DEGs be...
<p>Three RNA samples from the FlpIn-3T3 control cell line, three samples from the FlpIn-3T3 Pax6(5a)...