RNA-Seq Data Analysis    ◾    211

The expression level of a gene is described by the log-fold change of the gene transcript

abundance with respect to a reference. This reference will be a different gene in the case of

intra-sample comparison or the same gene in a different sample in the case of inter-sample

differential analysis. The significance of differential gene expression is measured by the

fold change, test statistic, p-value, adjusted p-value, and FDR. In the case of multiple com-

parison, the adjusted p-value is used. The expressed genes are usually sorted by p-values

(from the lowest to the largest) so that it will be easy to identify the top upregulated and

downregulated genes. These genes can be further analyzed by annotating them with their

GO and KEGG pathways terms to gain insight into their biological interpretation under

the conditions studied.

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