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Table 2 Excess of gene retention in parts of the vertebrate tree

From: The gain and loss of genes during 600 million years of vertebrate evolution

GOslim label, category, description Organism TPs showing significant difference TP with highest number of duplicates q-value
GO:0006118, BP, electron transport HS TP13 vs TP1 TP1 6.73E-05
  DR TP12 vs TP10 TP10 2.50E-04
  DR TP13 vs TP10 TP10 8.60E-06
GO:0006519, BP, amino acid and derivative metabolism HS TP13 vs TP1 TP1 8.69E-04
  DR TP12 vs TP10 TP10 5.37E-04
  DR TP13 vs TP10 TP10 1.47E-08
GO:0007165, BP, signal transduction TN TP13 vs TP11 TP13 5.76E-04
  XT TP13 vs TP8 TP13 9.18E-04
  RN TP13 vs TP2 TP13 1.44E-17
  MM TP13 vs TP3 TP13 8.32E-19
  HS TP13 vs TP1 TP13 2.43E-02
  DR TP12 vs TP10 TP10 3.60E-16
  DR TP13 vs TP10 TP10 6.40E-12
GO:0003677, MF, DNA binding XT TP13 vs TP8 TP13 4.38E-02
  RN TP13 vs TP2 TP13 1.20E-08
  MM TP13 vs TP3 TP13 1.86E-07
  DR TP12 vs TP10 TP10 1.51E-10
  DR TP13 vs TP10 TP10 3.99E-10
GO:0004872, MF, receptor activity TN TP13 vs TP11 TP13 6.34E-03
  XT TP13 vs TP8 TP13 5.83E-03
  RN TP13 vs TP2 TP13 2.26E-11
  MM TP13 vs TP3 TP13 7.47E-09
  DR TP12 vs TP10 TP10 1.01E-08
  DR TP13 vs TP10 TP10 7.37E-05
GO:0006464, BP, protein modification RN TP13 vs TP2 TP13 8.16E-12
  MM TP13 vs TP3 TP13 7.26E-07
  HS TP13 vs TP1 TP13 2.43E-02
  DR TP12 vs TP10 TP10 1.00E-09
  DR TP13 vs TP10 TP10 2.63E-07
GO:0005515, MF, protein binding TN TP13 vs TP11 TP13 5.76E-04
  XT TP13 vs TP8 TP13 1.01E-02
  RN TP13 vs TP2 TP13 2.31E-12
  MM TP13 vs TP3 TP13 3.72E-08
  DR TP12 vs TP10 TP10 7.78E-07
  DR TP13 vs TP10 TP10 4.01E-06
GO:0007275, BP, development TN TP13 vs TP11 TP13 3.71E-02
  XT TP13 vs TP8 TP13 4.50E-02
  RN TP13 vs TP2 TP13 7.64E-08
  MM TP13 vs TP3 TP13 1.49E-06
  HS TP13 vs TP1 TP13 1.88E-02
  DR TP12 vs TP10 TP10 1.18E-06
  DR TP13 vs TP10 TP10 1.06E-03
GO:0006350, BP, transcription TN TP13 vs TP11 TP13 1.97E-02
  RN TP13 vs TP2 TP13 7.13E-11
  MM TP13 vs TP3 TP13 3.82E-11
  DR TP12 vs TP10 TP10 1.54E-20
  DR TP13 vs TP10 TP10 4.11E-11
GO:0003723, MF, RNA binding RN TP13 vs TP2 TP2 4.71E-02
  HS TP13 vs TP1 TP1 9.08E-03
  DR TP12 vs TP10 TP10 9.36E-04
  DR TP13 vs TP10 TP10 3.42E-05
GO:0006811, BP, ion transport TN TP13 vs TP11 TP13 1.11E-02
  XT TP13 vs TP8 TP13 1.79E-02
  RN TP13 vs TP2 TP13 1.23E-11
  MM TP13 vs TP3 TP13 1.34E-06
  HS TP13 vs TP1 TP13 3.84E-02
  DR TP12 vs TP10 TP10 8.52E-03
  DR TP13 vs TP10 TP10 1.00E-02
  1. The GOslim label, its category (MF, molecular function; BP, biological process) and the general description are shown. For each organism (HS, human; MM, mouse; RN, rat; GG, chicken; XT, frog; DR, zebrafish; TN, Tetraodon), the number of species-specific duplicates was compared to the number of duplicates from time points (TPs) coinciding with WGDs (TP12 and TP13). The time points showing a significant difference (q < 0.05) in comparison are shown (TPx vs TPy), followed by the time point with the highest number of duplicates. The last column shows the q-value. Only significant results that are discussed in the text are listed (others can be found in Additional data file 1; Table S2).