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Table 1 Results from GENERATOR with H2O2 dataset using five clusters. The table shows the reported classes for five clusters from GENERATOR clustering shown in figure 1. The three over-representation values described in Methods section and figure 5 are reported for each class. Results are also compared to graphical output from SGD GO term finder (figure 8 [see Additional file 3]). Abbreviations in this column are: MF, molecular function; CC, cellular component; BP, biological process. Classes reported as 'missing' were not observed in the SGD GO term finder graphs. A more detailed view of the data is available in table 5 [see Additional file 5]. Classes with S.log(p) < 1 (marked with -) are not included to analysis although they are still shown here.

From: Theme discovery from gene lists for identification and viewing of multiple functional groups

CLUSTER FUNCTIONAL CLASS C.log(p) O.log(p) S.log(p) SGD
I organellar ribosome 46.7 26.1 21 CC
  mitochondrial ribosome 46.7 26.1 21 CC
  mitochondrial matrix 41.6 30.5 14.9 CC
  Ribosome 36.9 14.5 23.7 CC
  structural constituent of ribosome 35.9 14.8 22.3 MF
II RNA ligase activity 13.3 6.68 6.64 MF
  tRNA ligase activity 13.3 6.68 6.64 MF
  ligase activity, forming aminoacyl-tRNA and related compounds 13.3 6.68 6.64 MF
  ligase activity, forming carbon-oxygen bonds 13.3 6.68 6.64 MF
  ligase activity, forming phosphoric ester bonds 13 6.42 6.64 MF
III mitochondrial membrane 13.9 3.66 11 CC
  inner membrane 13.1 3.99 9.6 CC
  mitochondrial inner membrane 13.1 3.99 9.6 CC
  Mitochondrion 8.91 40.1 1.03 -
  respiratory chain complex III 8.03 4.32 3.74 CC
IV transcription regulator activity 12.3 2.52 11.5 MF
  nucleobase, nucleoside, nucleotide and nucleic acid metabolism 8.99 2.15 7.51 BP
  mediator complex 8.97 5.15 3.88 Missing
  general RNA polymerase II transcription factor activity 7.94 4.16 3.88 MF
  DNA-directed RNA polymerase II, holoenzyme 7.81 4.04 3.88 Missing
V mitochondrial genome maintenance 7.22 5.97 2.02 Missing
  mitochondrion organization and biogenesis 6.74 4.06 3.05 Missing
  mitochondrial chromosome 4.23 3.18 1.05 - (CC)
  soluble fraction 3.1 2.52 1.09 -
  helicase activity 3 3.35 0.79 -
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