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Fig 8. A few Xenopus laevis homeologous gene pairs display spatial subfunctionalization. We have studied how homeologous genes are expressed in the whole dataset (using weighted gene co-expression network analysis [WGCNA]) or in the dissected regions. We found that most pairs with differential expression exhibit asymmetrical decrease of 1 copy (e.g., egr4, sh3pxd2a, snail2, Fig 7, S11 Fig). We found 5 pairs with spatial differential expression, suggesting spatial subfunctionalizations: at Nieuwkoop and Faber stage (St.) 12.5, alas1, ccdc68, gmnc-like, and hs6st1 and at St. 14, p2ry1. Average and nonnegative matrix factorization (NMF) expression patterns are shown at the relevant stage.
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