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Super-pathway of melatonin degradation pathway was predicted to be the most frequently activated pathway by TBI. The top expression genes in this super-pathway were further analyzed for their expression patterns in the mRNA datasets of B. napus. The heatmaps were drawn using the R package.
Birdsong flowering pathway was predicted to be the most frequently inhibited pathway by TBI. The top expression genes in this pathway were further analyzed for their expression patterns in the mRNA datasets of B. napus. The heatmaps were drawn using the R package.
We identified HRD features in the breast cancer cell lines using the HRDetect algorithm, and the top six HRDetect-high cell lines were treated with carboplatin. However, there was no significant difference in sensitivity to carboplatin between the HRD index and HRDetect algorithms (Additional file 1: Table S1). Through analysis of the tumor-expressed BnabHLHs, we found that 34 of the 397 B. napus genes (87%) had similar expression patterns to those in A. thaliana, and this was the case for both the HRDetect-high and HRDetect-low subgroups. This is despite the fact that the B. napus genes were not derived from the HRDetect-high subgroup of the cell lines. In addition, on average, the expression profiles of the B. napus genes in the two subgroups were distinct from that of the germline genes, which suggests that the B. napus genes might be more responsive to platinum-based chemotherapy (Additional file 1: Figure S2).
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One of the drawbacks to this approach was that we needed to recompile every time we made even a small change to the code. This slowed everything else we were doing down and because we couldn't always have someone waiting for the application to finish building. 827ec27edc