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Table 2 Results of the pattern discovery and discriminant analysis for annotated complexes

From: Transcriptional regulation of protein complexes in yeast

  Annotated complex ORFs Coverage Max sig Discovered patterns
Permanent 26S proteasome 36 0.83 15.84 24
     19-22S regulator 18 0.94 8.76 16
     20S proteasome 15 0.87 5.76 13
  Respiration chain complexes     
     Cytochrome bc1 complex 9 0.67 1.13 4
     Cytochrome c oxidase 8 0.88 1.51 2
     F0-F1 ATP synthase 15 0.67 4.01 4
  Cytoplasmic ribosomes 138 0.68 19.49 151
     Cytoplasmic ribosomal large subunit 81 0.70 11.67 77
     Cytoplasmic ribosomal small subunit 57 0.79 8.97 63
  Cytoplasmic translation elongation 9 0.78 2.35 10
  Cytoplasmic translation initiation 27 0.19 6.31 5
     eIF3 7 0.43 1.24 2
  Nucleosomal protein complex 8 1.00 4.38 20
  RNA polymerase III 13 0.46 1.52 2
  RNA polymerase II holoenzyme 35 0.11 1.81 2
Transient Microtubules 32 0.16 1.45 5
  Pyruvate dehydrogenase 5 0.60 1.81 1
  Replication complexes     
     Replication complex 19 0.42 1.66 5
  SAGA complex 14 0.50 1 5
  Spindle pole body 32 0.13 2.93 8
     SPB components 16 0.25 3.38 8
  Tim22p complex 5 0.40 1.99 1
Others Cdc28p complexes 10 0.60 2 5
  H+transporting ATPase-vacuolar 15 0.40 2.46 6
  Nuclear splicing complexes-Spliceosome 66 0.06 1.55 5
  Other DNA repair complexes 5 0.40 1.11 4
  Replication complexes 49 0.41 15.64 7
     Replication fork complexes 30 0.57 13.28 12
  Respiration chain complexes 37 0.59 8.49 11
  rRNA processing complexes 18 0.22 1.72 2
  t-SNAREs 10 0.40 1.45 3
  1. Column 2 lists the names of the analyzed complexes. Columns 3 and 4 list, respectively, the number of components in the complex and the coverage of the assignment, defined as the fraction of the components of a given complex that are predicted to be part of a putative regulon. Max sig (column 5) is the highest significance index in patterns detected for this complex, and column 6 lists the number of discovered patterns for the complex. Complexes have been subdivided into three categories - 'permanent', 'transient' or 'others' - as indicated in column 1, and described in Materials and methods. Assemblies such as 'Respiration chain complexes', which contain several groups of complexes and hence do not represent a single physical entity, were classified here in the 'others' category. However, smaller complexes, which are part of this assembly and for which putative regulons were identified, were classified as 'permanent'.