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Table 3 Distribution of selected genes versus all S. cerevisiae genes

From: Large-scale exploration of growth inhibition caused by overexpression of genomic fragments in Saccharomyces cerevisiae

  All S. cerevisiae genes Percentage of total Selected toxic genes Percentage of total
Functional classes (MIPS data)     
Cell cycle_DNA processing 670 11.5 75 16.5*
Cell fate 486 8.4 66 14.5*
Cell rescue, defense and virulence 288 5.0 23 5.1
Cellular communication/signal transduction mechanism 59 1.0 6 1.3
Cellular transport and transport mechanisms 525 9.0 67 14.8*
Classification not yet clear-cut 112 1.9 6 1.3
Control of cellular organization 207 3.6 22 4.8
Energy 244 4.2 12 2.6
Metabolism 1,061 18.3 88 19.4
Protein fate (folding, modification, destination) 593 10.2 47 10.4
Protein synthesis 377 6.5 17 3.7*
Regulation of/interaction with cell. Environment 197 3.4 29 6.4
Transcription 801 13.8 88 19.4*
Transport facilitation 321 5.5 61 13.4*
Unclassified 1,706 29.4 91 20.0*
Cellular localization (MIPS data)     
Extracellular 54 1.4 5 1.6
Cell wall 38 1.0 4 1.3
Golgi 103 2.6 8 2.5
Transport vesicles 54 1.4 3 0.9
Plasma membrane 171 4.4 34 10.7*
Nucleus 1,367 34.8 130 40.8
Cytoplasm 2,001 50.9 137 42.9*
Peroxisome 42 1.1 3 0.9
Endosome 20 0.5 2 0.6
Cytoskeleton 154 3.9 22 6.9
Vacuole 82 2.1 8 2.5
Endoplasmic reticulum 353 9.0 27 8.5
Mitochondria 562 14.3 37 11.6
Viability (MIPS data)     
Essential 939 16.2 96 21.1
Essential or not 160 2.8 20 4.4
Phylogeny (Génolevures data)     
Conserved 3,717 64.1 336 74.0*
Ascomycete-specifics 1674 28.8 106 23.3*
Orphan 412 7.1 10 2.2*
  1. The distribution of genes was examined in respect of four classifications: function, cellular localization of the gene product, viability and phylogeny. Data are from MIPS [38] and Génolevures [37]. Cellular localization was known for 3,928 out of the 5,803 proteins in the entire genome and for 319 proteins out of the 454 that yield toxic inserts. For other comparisons, the set of 454 selected genes was compared to the set of 5,803 genes of S. cerevisiae. Note that a given gene may be present in more than one MIPS class. Significant evidence that a given gene class is over-or under-represented among toxic genes as compared to all S. cerevisiae genes is emphasized by bold characters. *p < 0.005; p < 0.025.