For a ⩾3-grade improvement in PGA and a ⩾50% improvement in NAPSI score, we separately investigated only the predictors because datasets for the complete ensemble of possible predictors were missing in >20% of patients with skin and nail lesions; thus, a selection bias could not be excluded.
An example is shown in Figure 5 (see Dataset S3 for the complete list).
We then reviewed available literature to predict the biological consequences of the observed G2-M gene regulations (228 in total; 114 with available genetic and/or biochemical data; Table 1 and Dataset S4b for the complete list of genes and references).
We ran twice 2 searches of four chains for 2 million generations each, sampled every 100 generations, for all datasets except for the complete frizzled-CRD data for which the same number of chains was run for 5 million generations.
The number of di-, tri- and tetra-nucleotide repeats identified in the Cucurbita unigene dataset is shown for the complete set of putative SSRs.
For the Sanger dataset, we used the complete dataset of 5 loci and subsets of 4 loci (removing CytB), 4 loci (removing COI), and 3 (nucDNA only) loci.
The sequence divergence among ingroup taxa ranged from 16.3 (ND6) to 23% (ND2) for the protein-coding dataset (average 20.4%), from 9.2 (12S rRNA) to 10.5% (16S rRNA) for the rRNA dataset (average 9.85%), 7.3% for the tRNA dataset, 11.4% for the control region, and 16.6% for the complete dataset.
In this study, SAM was used to identify differentially expressed genes for the complete dataset and the imputed dataset.
The complete dataset for the standard sequences is available as supplementary material (see Additional files 3 and 4).
When 13'379 fast-evolving positions were removed, the LG-based analysis converged with high support (94% BP; 0.99 PP) towards the topology that was weakly suggested by the CAT-based analysis of the complete dataset for the association of Phytomyxea, Gromia, Foraminifera and Acantharea, before diverging likely due to lack of phylogenetic signal in the shortest alignments.
