The results show good robustness properties of the proposed method against all the tested attacks except for the thresholding and Wiener filtering.
These results suggest that N2O3 does not affect the bistable character of the response to EC stimuli, except for modifying the threshold for onset of apoptosis, which is shifted to higher [casp8]0 (i.e. rendered more difficult) with decreasing [GSH]0.
Most settings were not varied throughout the test runs except for the tracking threshold of PG that was set more stringent than its default value, unless indicated otherwise.
Although the log-normal assumption would seem to apply more naturally to the apical response itself, a log-normal distribution for the apical response is incompatible with a log-normal distribution for the threshold (except under highly restrictive conditions).
Except for the significance thresholds, each of the tests was made in exactly the same manner as for a single pair.
These thresholds are generally higher than in Table 4 (i.e. favor the focal female less) because the benefit is going to a female coeval instead of to self (except for the maternal thresholds, which are identical because it is the same fitness tradeoff from the mother's point of view).
SDREM outperforms the gene prioritization tools at all thresholds except for the top 20 threshold where Pinta makes the same number of correct predictions and Endeavour makes two more.
Adapter removal and quality trimming were performed with the tool AdapterRemoval using the default parameters except the threshold for trimming low quality bases (Q < 10), meaning that consecutive stretches of bases from both the 5' and 3' end of the reads with Phred Quality of 10 or lower were trimmed, and the minimum read length set to 30 nucleotides.
To identify enriched domains we used MACS version 2.0.10.20131028 with default parameters35, except for the p-value threshold that was set at p < 10−5.
