We provide an alternative scoring method to account for multiple genes (Supplementary Notes) that produces similar results in four traits we tested (Supplementary Fig. S4).
To investigate this aspect of the water-to-land transition, we identified 684 genes (657 genes possess transcript evidence; see Supplementary Note 5) that are present in mudskippers but not in other analyzed teleosts.
Accuracy (y axis) is shown across varying expression noise levels (x axis) for different methods: CPM (black) and an enrichment scheme ('ES'; see implementation in Supplementary Note 1) that was applied using reference data of varying granularity (2 to 20; color coded).
For the purpose of comparison with results presented in Kocsor et al. (2006) the classification results of the CSSS model are expressed as the integral of the AUC curve shown in Supplementary Figure S2 in Supplementary Data (note that since Dataset III contains 54 families the maximum value for this integral is 54).
Different mathematical terms and other term combinations to dissect the pro-inflammatory effects responsible to impair bacterial clearance are summarized in Table 1 and Supplementary 3. Note that the purpose of our in silico work was not biological quantification of the experiments but using a model selection process to provide mechanistic insights into coinfection.
This file contains Supplementary Notes 1-11, Supplementary Figures 1-11 and Supplementary Table 1-11 (please note that Supplementary Tables 3, 4, 8 and 9 are in a separate excel file) - see pages 1-7 for more details of the Content.
FPKM cutoffs for each sample were determined based on FPKM values for introns and intergenic regions (see supplementary fig. S5, Supplementary Material online; note that the results are insensitive to different FPKM cutoffs, supplementary figs. S6 and S7, Supplementary Material online).
A detailed examination of TepI revealed a major deletion of four exons in D. sechellia, which are all present in the remaining species (supplementary fig. S3, Supplementary Material online, note that the predicted gene product did not fully correspond to our sequenced transcript).
S1 S6, Supplementary Material online; note that one of the analyses shown in supplementary fig. S6, Supplementary Material online, considered only taxa in Dioscoreales and Pandanales).
A further discussion on the characteristics of the observed emitters is given in the Supplementary Note 9. We note that to demonstrate coupling between emitter and the optical mode, both spatial and spectral matching are required.
