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Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis

Fig 5

Validation by comparison with qRT-PCR results.

(A) The scatter plots compare the reported relative proportion of each pair of the isoforms of each gene between the computational methods (Net-RSTQ, base EM, Cufflinks, and RSEM) and qRT-PCR experiments. The proportions of the two compared isoforms in a pair are normalized to adding to 1. The x-axis and y-axis are the relative proportion of one of the two isoform (the other is 1 minus the proportion) reported by qRT-PCR and the computational methods, respectively. The scatter points aligning closer to the diagonal line indicate better estimations by a computational method matching to the qRT-PCR results. The unshaded gradient around the diagonal line shows the regions with scatter differences less than 0.1, 0.15, 0.2 and 0.25, within which the estimations are more similar to the qRT-PCR results. (B)-(D) The scatter plots on each individual dataset. (E) The table shows the percentage of predictions by each method within the unshaded regions and the overall Root Mean Square Error of the predictions by each method compared to the qRT-PCR results.

Fig 5

doi: https://doi.org/10.1371/journal.pcbi.1004465.g005