Fig. 2: Kinases driving the phosphoprofiles of responders to paclitaxel.

Panel A displays the significantly enriched kinases found in the baseline samples for patients who achieved a pCR in the paclitaxel monotherapy arm. However, Panel B shows that when the analysis was repeated combining the samples from the paclitaxel-only arm with those from the combination arm, virtually no significant enrichment was observed. For all KSEA plots, each vertical black line represents a phosphopeptide that can be phosphorylated by the depicted kinase that was detected in the samples from one of the compared conditions in the KSEA. High in responders and high in nonresponders refers to the increased abundance of phosphopeptides in the baseline samples of patients who achieved a pCR or patients who did not achieve a pCR, respectively. NES (normalized enrichment score) and FDR (false-discovery rate) values are depicted for each KSEA. A relaxed FDR boundary (up to 0.20) was allowed to ensure as little information loss as possible in the mass spectrometry-to-immunohistochemistry translation step, since the biomarker candidates underwent a subsequent 2-patient series filter.