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Figure 6 | BMC Genomics

Figure 6

From: Transcriptomic portrait of human Mesenchymal Stromal/Stem cells isolated from bone marrow and placenta

Figure 6

Analysis of differential expression on the RNA-Seq data of BM- and PL-MSCs. Scatter plots marking in red the significant genes found with two different methods: (A) Cuffdiff and (C) DEseq. Volcano plots of the expression data analyses done (B) using Cuffdiff and (E) using DEseq. Setting the q-value threshold at < 0.05 (blue line) for both methods, they detect 232 and 2627 significant genes, respectively. Since DEseq method is much less stringent than Cuffdiff and to avoid false positives, a second cut-off at q-value < 0.001 was set up for DEseq differential expression, selecting in this way 1388 significant genes. (D) Figure showing a proportional Venn diagram to illustrate the overlap of the genes selected by Cuffdiff (232) and DEseq (1388). The overlap includes 203 genes that undergo significant differential expression changes (i.e. common genes in red, in the scatter plots 6A and 6C).

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