Table 2. Gene ontology (GO) Biological Process (BP) terms associated with the upregulated and downregulated differentially expressed genes in the honeybees of the larval feeding NGS experiments (only the top 10 over-represented GO PB terms with the lowest p-values are shown).

GO term	P-value	Sample frequency	Background frequency
Contrast 3
Upregulated DE genes
GO:0006412 translation	3.31E–05	31/186 (16.7%)	787/14,580 (5.4%)
GO:0044237 cellular metabolic process	1.87E–04	96/186 (51.6%)	4,811/14,580 (33.0%)
GO:0009161 ribonucleoside monophosphate metabolic process	2.16E–04	12/186 (6.5%)	132/14,580 (0.9%)
GO:0009123 nucleoside monophosphate metabolic process	2.35E–04	12/186 (6.5%)	133/1,580 (0.9%)
GO:0046034 ATP metabolic process	3.67E–04	11/186 (5.9%)	113/14,580 (0.8%)
GO:0032543 mitochondrial translation	6.05E–04	6/186 (3.2%)	23/14,580 (0.2%)
GO:0009167 purine ribonucleoside monophosphate metabolic process	1.11E–03	11/186 (5.9%)	126/14,580 (0.9%)
GO:0009126 purine nucleoside monophosphate metabolic process	1.11E–03	11/186 (5.9%)	126/14,580 (0.9%)
GO:0010467 gene expression	4.08E–03	56/186 (30.1%)	2,397/14,580 (16.4%)
GO:0044249 cellular biosynthetic process	5.38E–03	56/186 (30.1%)	2,418/14,580 (16.6%)
Downregulated DE genes
None
Commonality between Contrasts 2, 4, and 5
Upregulated DE genes
GO:0050896 response to stimulus	1.11E–10	104/263 (39.5%)	2,855/14,580 (19.6%)
GO:0006950 response to stress	3.34E–10	57/263 (21.7%)	1,084/14,580 (7.4%)
GO:0002376 immune system process	1.04E–09	33/263 (12.5%)	405/14,580 (2.8%)
GO:0006952 defense response	9.74E–08	29/263 (11.0%)	373/14,580 (2.6%)
GO:0044699 single-organism process	6.35E–07	194/263 (73.8%)	8,031/14,580 (55.1%)
GO:0006955 immune response	2.61E–06	24/263 (9.1%)	298/14,580 (2.0%)
GO:0065007 biological regulation	5.27E–06	109/263 (41.4%)	3,621/14,580 (24.8%)
GO:0044763 single-organism cellular process	7.96E–06	154/263 (58.6%)	5,930/14,580 (40.7%)
GO:0045087 innate immune response	6.92E–05	16/263 (6.1%)	157/14,580 (1.1%)
GO:0044707 single-multicellular organism process	2.72E–04	115/263 (43.7%)	4,170/14,580 (28.6%)
Downregulated DE genes
GO:0042335 cuticle development	3.78E-12	27/242 (11.2%)	234/14,580 (1.6%)
GO:0040003 chitin-based cuticle development	7.15E–11	23/242 (9.5%)	182/14,580 (1.2%)
GO:0030239 myofibril assembly	8.95E–10	12/242 (5.0%)	37/14,580 (0.3%)
GO:0055002 striated muscle cell development	6.24E–08	12/242 (5.0%)	51/14,580 (0.3%)
GO:0055001 muscle cell development	6.24E–08	12/242 (5.0%)	51/14,580 (0.3%)
GO:0031032 actomyosin structure organization	2.26E–07	13/242 (5.4%)	70/14,580 (0.5%)
GO:0006030 chitin metabolic process	3.65E–07	16/242 (6.6%)	122/14,580 (0.8%)
GO:1901071 glucosamine-containing compound metabolic process	1.07E–06	16/242 (6.6%)	131/145,80 (0.9%)
GO:0006040 amino sugar metabolic process	1.21E–06	16/242 (6.6%)	132/14,580 (0.9%)
GO:0006022 aminoglycan metabolic process	5.98E–06	16/242 (6.6%)	147/14,580 (1.0%)