Table 1 Cuticular collagen genes were up-regulated in npr-8(ok1439) animals relative to wild-type animals exposed to P. aeruginosa.

A. Enrichment of molecular functions revealed by GO analysis of up-regulated genes in npr-8(ok1439) animals relative to wild-type animals exposed
to P. aeruginosa.
GO termDescriptionP*FDR qEnrichment (N, B, n, b)
GO:0042302Structural constituent of cuticle3.08 × 10−86.87 × 10−57.96 (10,359, 121, 129, 12)
B. Enrichment of cuticular collagen genes in npr-8(ok1439) animals relative to wild-type animals with or without exposure to P. aeruginosa.
Enriched collagen
genes
Infected with P. aeruginosaUninfected
npr-8(ok1439) animals relative to wild-type animalsnpr-8(ok1439) animals relative to wild-type animals
Fold changeAdjusted P§Significantly
different?
Fold changeAdjusted P§Significantly
different?
col-934.63.75 × 10−82Yes1.32.82 × 10−2Yes
col-803.52.03 × 10−38Yes1.32.17 × 10−2Yes
col-1792.51.31 × 10−22Yes1.21.09 × 10−1No
col-982.46.85 × 10−22Yes1.34.35 × 10−2Yes
col-1602.49.91 × 10−33Yes1.41.37 × 10−3Yes
col-1242.42.97 × 10−14Yes1.29.33 × 10−2No
col-1032.21.35 × 10−17Yes1.33.74 × 10−2Yes
col-1012.18.11 × 10−14Yes1.21.78 × 10−4Yes
col-1462.09.72 × 10−8Yes3.39.24 × 10−23Yes
col-1592.01.20 × 10−6Yes1.83.05 × 10−6Yes
col-202.02.13 × 10−16Yes1.34.75 × 10−2Yes
Y69H2.142.01.13 × 10−14Yes1.36.05 × 10−2No

*P value is the enrichment P value computed according to the mHG model (Eden et al. 2007 PLoS Comp Bio 3 (3):e39).

†FDR q value is the correction of the above P value for multiple testing using the Benjamini and Hochberg method (Benjamini and Hochberg 1995 J R Statist Soc B 57 (1):289–300).

‡Enrichment (N, B, n, b) is defined as follows: N, total number of genes; B, total number of genes associated with a specific GO term; n, number of genes in the target set; b, number of genes in the intersection; Enrichment = (b/n)/(B/N).

§Adjusted P value is the correction of the P value for multiple testing using the Benjamini and Hochberg method (Benjamini and Hochberg 1995 J R Statist Soc B 57 (1):289–300).