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Table 1 Over-represented and under-represented functional annotations within the different duplicate sets

From: All duplicates are not equal: the difference between small-scale and genome duplication

GO ID Description Total observed P (raw) P (corrected)
Over-represented in set of WGDs
   0004672 Protein kinase activity 127 52 2.7 × e-12 <0.001
   0003735 Structural constituent of ribosome 217 72 3.4 × e-11 <0.001
   0016773 Phosphotransferase activity, alcohol group as acceptor 171 61 3.9 × e-11 <0.001
   0016301 Kinase activity 197 67 4.9 × e-11 <0.001
   0004674 Protein serine/threonine kinase activity 69 32 1.1 × e-09 <0.001
   0016772 Transferase activity, transferring phosphorus-containing groups 294 78 4.3 × e-07 <0.001
   0016538 Cyclin-dependent protein kinase regulator activity 23 14 8.8 × e-07 <0.001
   0005198 Structural molecule activity 338 83 5.6 × e-06 0.001
   0030234 Enzyme regulator activity 180 50 1.4 × e-05 0.002
   0019887 Protein kinase regulator activity 44 18 4.3 × e-05 0.004
   0016740 Transferase activity 641 135 4.6 × e-05 0.004
   0005083 Small GTPase regulator activity 47 18 1.2 × e-04 0.018
   0019207 Kinase regulator activity 47 18 1.2 × e-04 0.018
   0035251 UDP-glucosyltransferase activity 13 8 2.0 × e-04 0.027
   0003704 Specific RNA polymerase II transcription factor activity 45 17 2.2 × e-04 0.029
   0016791 Phosphoric monoester hydrolase activity 88 27 2.4 × e-04 0.029
   0030508 Thiol-disulfide exchange intermediate activity 8 6 2.9 × e-04 0.042
Under-represented in set of WGDs
   0008757 S-adenosylmethionine-dependent methyltransferase activity 62 0 2.7 × e-05 <0.001
   0016741 Transferase activity, transferring one-carbon groups 84 2 8.7 × e-05 0.003
   0015078 Hydrogen ion transporter activity 54 0 1.1 × e-04 0.006
   0008168 Methyltransferase activity 82 2 1.2 × e-04 0.006
   0031202 RNA splicing factor activity, transesterification mechanism 51 0 1.8 × e-04 0.008
   0016251 General RNA polymerase II transcription factor activity 62 1 3.4 × e-04 0.014
Over-represented in set of SSDs
   0051119 Sugar transporter activity 25 22 2.7 × e-20 <0.001
   0015144 Carbohydrate transporter activity 30 23 1.5 × e-18 <0.001
   0015145 Monosaccharide transporter activity 21 18 2.3 × e-16 <0.001
   0015149 Hexose transporter activity 21 18 2.3 × e-16 <0.001
   0015578 Mannose transporter activity 15 15 3.0 × e-16 <0.001
   0005353 Fructose transporter activity 15 15 3.0 × e-16 <0.001
   0017111 Nucleoside-triphosphatase activity 243 65 7.3 × e-16 <0.001
   0005355 Glucose transporter activity 18 16 3.5 × e-15 <0.001
   0016818 Hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides 264 67 4.4 × e-15 <0.001
   0016462 Pyrophosphatase activity 264 67 4.4 × e-15 <0.001
   0016817 Hydrolase activity, acting on acid anhydrides 264 67 4.4 × e-15 <0.001
   0005215 Transporter activity 410 84 6.7 × e-13 <0.001
   0003824 Catalytic activity 1885 252 7.3 × e-13 <0.001
   0016887 ATPase activity 185 46 2.5 × e-10 <0.001
   0016787 Hydrolase activity 707 109 2.1 × e-08 <0.001
   0016614 Oxidoreductase activity, acting on CH-OH group of donors 75 24 3.2 × e-08 <0.001
   0016616 Oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor 67 22 7.2 × e-08 <0.001
   0004386 Helicase activity 83 24 2.8 × e-07 <0.001
   0042626 ATPase activity, coupled to transmembrane movement of substances 58 19 5.9 × e-07 <0.001
   0043492 ATPase activity, coupled to movement of substances 58 19 5.9 × e-07 <0.001
   0016820 Hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances 58 19 5.9 × e-07 <0.001
   0016491 Oxidoreductase activity 262 49 1.2 × e-06 <0.001
   0015075 Ion transporter activity 145 32 2.6 × e-06 <0.001
   0008324 Cation transporter activity 124 28 6.9 × e-06 <0.001
   0042623 ATPase activity, coupled 125 28 8.2 × e-06 0.001
   0018456 Aryl-alcohol dehydrogenase activity 8 6 1.5 × e-05 0.002
   0015294 Solute:cation symporter activity 8 6 1.5 × e-05 0.002
   0003924 GTPase activity 54 16 2.0 × e-05 0.002
   0005354 Galactose transporter activity 6 5 3.9 × e-05 0.009
   0015293 Symporter activity 9 6 4.3 × e-05 0.012
   0005537 Mannose binding 4 4 7.6 × e-05 0.017
   0015238 Drug transporter activity 15 7 2.0 × e-04 0.035
   0003678 DNA helicase activity 35 11 2.2 × e-04 0.039
Under-represented in set of SSD
   0003676 Nucleic acid binding 494 12 1.8 × e-10 0
   0005488 Binding 1034 58 1.1 × e-06 0
   0003723 RNA binding 231 4 1.6 × e-06 0
   0003677 DNA binding 220 6 8.0 × e-05 0.002
   0030528 Transcription regulator activity 326 14 3.3 × e-04 0.006
   0016779 Nucleotidyltransferase activity 80 0 3.7 × e-04 0.009
  1. GO, Gene Ontology; SSD, small-scale duplicate; WGD, whole-genome duplicate.