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Table 3 explains the scenarios considered for subsequent experiments.
In this study a threshold was set at an Im of 5 and only proteins with an Im>5 were considered for subsequent cluster analyses.
Only probe sequences exhibiting a methylation ratio above 75% for the fully methylated control, together with less than 25% for the unmethylated control were considered for subsequent analysis.
Faeces that could not be properly assigned to any carnivore species were classified as 'non-identified', but also considered for subsequent analysis (see below).
Only genes with a relative expression ratio greater than 2.5 at t0 or at t2, and a significance value (p) smaller than 0.2, were considered for subsequent analysis.
Genes from the data set that were associated with a canonical pathway in the Ingenuity Pathways Knowledge Base were considered for subsequent analysis.
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From the confidence gained from the validation study, two fire scenarios, namely, fire at the ground floor and fire at the top floor, are considered for the subsequent parametric study.
Three different gene lists were considered for the subsequent enrichment analysis: all unique, annotated genes reported (1475 genes) (Table S2); those genes reported in at least two GEP studies (124 genes) (Table S1); and the ones which additionally showed the same direction in gene expression change, either up- or down-regulation, in two GEP studies (54 genes) (Table S1).
Multiple hits were removed, and only single best hits were considered for the subsequent analyses.
In particular, only the reads that are optimal for a given allele are considered for the subsequent analysis.
As short insertions and deletions are difficult to call in general, only SNPs were considered for all subsequent analysis.
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