Table 5. Enrichment analysis of LIN-29 target genes.

All LIN-29-regulated targets (n = 1101)		Gene count
Category/GO term		In genome	Found	Expected	Fold	P value
GO biological process	Peroxisome organization	18	7	0.97	7.23	1.89E−04
	Fatty acid metabolic process	105	21	5.65	3.72	1.56E−06
	Defense response to Gram-positive bacterium	60	12	3.23	3.72	2.65E−04
	Innate immune response	345	57	18.56	3.07	2.55E−12
	Oxidation-reduction process	618	60	33.25	1.8	3.76E−05
	Cellular response to chemical stimulus	612	57	32.92	1.73	1.57E−04
GO molecular function	Structural constituent of cuticle	168	48	9.04	5.31	2.90E−18
	Iron ion binding	118	20	6.35	3.15	2.38E−05
	Oxidoreductase activity	539	56	29	1.93	1.08E−05
GO cellular component	Peroxisomal membrane	18	8	0.97	8.26	3.08E−05
	Membrane raft	80	14	4.3	3.25	2.87E−04
	Extracellular space	294	37	15.82	2.34	7.31E−06
Lipid metabolisma	N/A	471	65	25.33	2.56	1.72E−12

1.7-fold upregulated targets (n = 230)		Gene count
Category/GO term		In genome	Found	Expected	Fold	P value
GO molecular function	Structural constituent of cuticle	168	33	1.9	17.36	5.46E−29
Lipid metabolisma	N/A	471	2	5.29	0.94	6.84E−02

1.7-fold downregulated targets (n = 350)		Gene count
Category/GO term		In genome	Found	Expected	Fold	P value
GO biological process	Fatty acid metabolic process	105	11	1.79	6.16	3.99E−06
	Innate immune response	345	18	5.87	3.07	4.40E−05
GO cellular component	Peroxisomal membrane	18	5	0.31	16.34	3.33E−05
Lipid metabolisma	N/A	471	25	8.05	3.11	4.61E−07

Enrichment analyses were done for all LIN-29 significant targets and for both 1.7-fold LIN-29 up- and downregulated subsets using Gene Ontology (GO) Consortium (see Materials and Methods).

^aGenes were also compared to the list of 471 C. elegans metabolic genes from Y. Zhang et al. (2013).