Table 7. Aplysia co-expression module enrichment for orthologs differentially expressed after immune priming and viral challenge in pacific oyster Crassostrea gigas.
| Aplysia transcripts in C. gigas (m+n) | Transcripts in LaFont (m) | Transcripts not in Lafont (n) | signif threshold (ɑ) | Bonferroni (ɑ`= ɑ/14) | |
|---|---|---|---|---|---|
| 7359 | 697 | 6662 | 0.05 | 0.00385 | |
| Module | Transcripts in module (k) | Module transcripts in LaFont (x) | Proportion (x/k) | p-value (p = Σp(x-1:k)) | Sig (p<ɑ`) |
| greenyellow | 224 | 45 | 0.20 | 4.37E-06 | * |
| darkgreen | 156 | 29 | 0.19 | 1.41E-03 | * |
| pink | 906 | 111 | 0.12 | 3.71E-03 | * |
| purple | 2203 | 206 | 0.09 | 6.72E-01 | - |
| blue | 1170 | 109 | 0.09 | 6.78E-01 | - |
| violet | 24 | 2 | 0.08 | 1.00E+00 | - |
| royalblue | 410 | 34 | 0.08 | 9.01E-01 | - |
| grey | 190 | 15 | 0.08 | 9.22E-01 | - |
| green | 1838 | 133 | 0.07 | 1.00E+00 | - |
| orange | 125 | 9 | 0.07 | 9.59E-01 | - |
| steelblue | 39 | 2 | 0.05 | 1.00E+00 | - |
| paleturquoise | 23 | 1 | 0.04 | 1.00E+00 | - |
| saddlebrown | 51 | 1 | 0.02 | 1.00E+00 | - |
Module enrichment for C. gigas immune genes in Aplysia co-expression modules was assessed via Fisher’s exact test. Of the 7359 Aplysia transcripts that were annotated as C. gigas orthologs and present in Aplysia co-expression modules, 697 were present in C. gigas (Lafont et al (2020) [37] m = 697, n = 6662). For each module, the number of transcripts in that module that were marked as C. gigas orthologs (k) and the proportion of those also present in Lafont et al (2020) [37] (x) were used to calculate the hypergeometric distribution in R. The p value was calculated as the sum of all probabilities at least as extreme as k (Σp(x-1:k) which was compared to a significance threshold of 0.05 with Bonferroni multiple test correction for 14 tests. Three modules (greenyellow, darkgreen, and pink) were identified as significantly enriched for C. gigas immune response orthologs.