Table 2.
Gene content in X. tropicalis genes within LLT-triplets compared to the reference set of all X. tropicalis genes with X. laevis orthologs.
| Molecular function | Number within referenceSet | Number within LLT triplets | Expected based on reference | Over- or Under-represented (±) | p-Value |
| Transfer/carrier | 123 | 46 | 29.11 | + | 0.06 |
| Membrane traffic | 165 | 57 | 39.05 | + | 0.107 |
| Defense/immunity | 90 | 10 | 21.3 | - | 0.146 |
| Ribosomal | 105 | 42 | 24.85 | + | 0.154 |
| Hydrogen transporter | 24 | 14 | 5.68 | + | 0.44 |
| Select regulatory molecule | 479 | 135 | 113.36 | + | 0.625 |
| Receptor | 309 | 57 | 73.13 | - | 0.787 |
| Nucleodityltransferase | 35 | 8 | 8.28 | - | ~1 |
| Double-stranded DNA binding | 10 | 2 | 2.37 | - | ~1 |
| Transferase | 431 | 91 | 102.00 | - | ~1 |
Genes were categorized by assigning PANTHER classification terms to our X. tropicalis gene set by HMM scanning of the peptides and then grouping the terms into high-level categories of molecular function. We were able to assign categories to 6393 genes in the reference set and to 1513 genes in the subset. Out null hypothesis is that the second copy of genes following the X. laevis tetraploidization are lost in a random fashion. None of the 10 categories shown here show significant deviation from the null hypothesis, and the remaining molecular categories all have p-values close to 1. All p-values were Bonferroni-corrected for multiple tests.