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About Gene Significance
Gene expression (RPKM), log-fold change relative to control liver, and significance were calculated using the DESeq software package. Individual gene transcripts were considered de-regulated if the false discovery rate adjusted p-value (q-value) was less than 0.05.
For the samples Tumor (T), Regression Day 3 (R3), and Recurrent Tumor (RT), the total number of significantly de-regulated transcripts exceeded 5000, which is the maximum capacity for pathway analysis using Ingenuity Pathway Analysis. In order to decrease the number of genes included in the pathway analysis, a subset of these genes was used according to the following criteria:
- Day 3: q-value < 0.05 (266 genes)
- Day 7: q-value < 0.05 (742 genes)
- Tumor: q-value < 0.01 and |log2-fold change| > 1.4 (8846 -> 4801 genes)
- Regression Day 3: q-value < 0.01 (6299 -> 4774 genes)
- Regression Day 7: q-value < 0.05 (4182 genes)
- Tumor: q-value < 0.01 and |log2-fold change| > 1.3 (8846 -> 4796 genes)