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Screen conditions were in principle similar to methods described earlier [39], with modifications described below.
To estimate expression profiles as continuous functions over time, we used cubic B-spline smoothing models, following methods previously established for microarray data [26], [27], [28] with the modifications described below and in Fig. S2.
BMP tests were performed as reported elsewhere [ 31], with the modifications described below.
The ribosomal profiling technique was carried out according to Ingolia et al. (2012) but with important modifications described below.
Dehalobium chlorocoercia DF-1 was grown anaerobically in mineral medium (E-Cl) as described previously with modifications described below.
The technique used in this study is similar to the one presented previously [ 22] with minor modifications described below.
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To link to PRIDE's modification location table described below, a two-filter/attribute importable and exportable were defined using the shared UniProt and PSI-MOD IDs, while to link to the COSMICMart data set, the two-filter/attribute values were based on shared UniProt ID and modified/mutated residue position.
The basic principles of the methods described below are the same, while modifications thereof will be presented in the sections dedicated to specific sample types.
However, the basic hypothesis-testing framework described below could be used with only trivial modification.
Bonding interface properties were evaluated as proposed in section 8.F of DNV RP, with some modifications as described below.
Network analysis was largely carried out as described previously [3], with modifications as described below.
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