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Table 2 Gene content in X. tropicalis genes within LLT-triplets compared to the reference set of all X. tropicalis genes with X. laevisorthologs.

From: Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis

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
  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.