Table 5.
Enrichment analysis of genes that were significant for pretreatment or strain-by-pretreatment interaction in the ILS/ISS time course. Genes for all three time points were included in the analysis.
| Annotation cluster #1 | Representative Terms (GOTERM_BP_FAT)1 |
|---|---|
| 2 (7.3); 4 (4.0); 18 (2.0); 53 (NS) |
Regulation of transcription (238) Positive regulation of transcription (65) Positive regulation of transcription from RNA polymerase II promoter (44) RNA processing (56) |
| 8 (2.8) |
Chromosome organization (51) Chromatin modification (31) |
| 10 (2.5) |
Protein catabolic process (61) Proteolysis involved in cellular protein catabolic process (59) |
| 12 (2.3); 17 (2.0) |
ncRNA processing (28) Ribosome biogenesis (18) |
| 13 (2.3) |
Regulation of apoptosis (60) Positive regulation of apoptosis (32) Induction of apoptosis (25) |
| 22 (1.8) |
Negative regulation of catalytic activity (17) Negative regulation of transferase (11) |
| 23 (1.8) |
Establishment of protein localization (71) Intracellular transport (50) |
| 25 (1.7) | Protein amino acid dephosphorylation (20) |
| 27 (1.6) | Small GTPase mediated signal transduction (34) |
| 37 (1.4) | Cerebral cortex development (9) |
1
Number in parentheses is the Enrichment Score for each cluster; score 1.3 is equivalent to non-log scale p of 0.05 (Huang et al., 2009). In two cases, distinct clusters contained similar terms; these have been grouped here (see supplemental Table S-2). NS: Enrichment Score < 1.3.
2
Number in parentheses indicates the number of genes found within that term; terms are from GOTERM_BP_FAT.