Differential Expression Analysis (DE) as obtained by EdgeR.

Column headers as follows: TRANSCRIPT_ID, ID as from the Rockefeller A5 dataset; sampleA and sampleB, samples compared; logFC, log2 fold change (log base 2 of the fold change in gene expression between the two experimental conditions); logCPM, log2 counts per million (log base 2 of the normalized expression levels for a given gene across all samples); Pvalue, probability that the observed difference in gene expression occurred by chance under the null hypothesis; FDR, false discovery rate (multiple testing corrected P value using the Benjamini-Hochberg method; when FDR ≤ 0.05, the gene is considered significantly differentially expressed after adjusting for multiple comparisons). FPKM, Fragment per Kilobase per Million Reads, of the different replicates are also reported. The different comparisons are reported in the different worksheets as indicated: T1 and T5, 1 dpi and 5 dpi; Mi_V and Mi_C, infected and uninfected midguts; Ca_V and Ca_C, infected and uninfected carcasses; UP, upregulated. (XLSX)