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The frequency of a KEGG pathway hit by an environmental sequence cluster is calculated by the number of individual sequences divided by the total number of sequences in each environmental dataset.
Resulting effects rely again on the multiple pathway hit strategy built into MB.
Hence, we chose to include any pathway hit in the annotation, even if only fewer enzymes were captured in sequencing.
The above alterations, identified in the era before next-generation sequencing, were together seen to account for the MAPK pathway "hit" in around 80 90 % of PAs.
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More pathway hits below a defined cutoff will correlate with the entire distribution shifting toward lower concentrations.
We also found pathway hits for calcium signaling, CREB pathway, IL2 and IL12 which were also found in Torkamani [ 23] and Wang et al. [ 9].
Figure 4 shows the correlation between the number of pathway hits and the minimum AC50/LEC for cytotoxicity across the 15 assays.
The conazoles and triazoles (many of which overlap) and pyrethroids show the broadest activity spectrum, with median number of pathway hits of around 10 of the 33 minimal pathways.
Recently, Zhang et al. and Jones et al. described MAPK pathway hits in 95 to 100% of PAs, demonstrating the central importance of targeting specific pathway alterations in this tumor type [ 20, 21].
Top pathway hits include Focal Adhesion (18 genes), Extra-Cellular Matrix (ECM) Receptor Interactions (15 genes), Cell Communication (15 genes), and Regulation of Actin Cytoskeleton (12 genes) [see Additional file 4].
In addition, the sign of the association was correct in all cases: The higher the number of low-concentration in vitro pathway hits, the lower the observed lowest toxic dose in vivo.
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