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Table 1 Datasets

From: Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

Source Dataset Pass filter? Genes Relationships
Genetic interactions     
   FlyBase All reported GIs N/A 2,878 6,941
Protein-protein interactions     
   BIND, DIP, IntAct Direct assay N/A 935 1,234
   DroID, BioGRID High-confidence Y2H N/A 4,543 4,590
  Positive Y2H N/A 6,183 19,584
Microarray     
   Hooper et al. [100] All conditions Yes 10,460 3,289,275
   Chintapalli et al. [102] All conditions Yes 10,054 3,618,216
   Parisi et al. [92] All conditions Yes 9,922 5,656,854
   Edwards et al. [99] Line1 Yes 8,403 8,072,394
  Line2 Yes 8,296 8,118,665
  All conditions Yes 0 0
   Altenhein et al. [98] All conditions Yes 8,341 1,030,457
  Gof No 0 0
  Lof No 0 0
   Hild et al. [97] All conditions Yes 8,214 677,746
   Qin et al. [94] All conditions Yes 6,734 4,187,496
   Tomancak et al. [103] All conditions Yes 6,288 2,626,310
   Magalhaes et al. [59] All conditions Yes 5,718 1,102,629
   De Gregorio et al. [57] All conditions Yes 5,698 1,561,265
  Bacteria Yes 4,920 237,361
  Fungus No 0 0
  Spaetzle No 0 0
  Relish No 0 0
  Spaetzle &relish No 0 0
   Sandmann et al. [101] All conditions Yes 5,474 1,238,924
   Arbeitman et al. [61] All conditions Yes 4,354 1,769,479
  Embryo Yes 4,126 1,271,286
  Larva No 0 0
  Pupal No 0 0
  Adult male No 0 0
  Adult female No 0 0
   Sorensen et al. [96] Heat Yes 4,219 690,181
  No heat Yes 4,083 701,546
  All conditions Yes 0 0
   Beckstead et al. [95] Third instar Yes 4,015 1,000,994
   Estrada et al. [93] All conditions Yes 2,978 657,929
   Wertheim et al. [58] All conditions Yes 2,280 551,684
   Beckstead et al. [95] Ecr No 0 0
   Li et al. [91] All conditions No 0 0
  1. List of all datasets used in this study. The unit of data which we call a dataset is contained in the 'dataset' column. The filtering criteria apply to the microarray data as described in the Materials and methods section. The number of unique genes and functional relationships that a dataset contributes to the integrated network are listed. A '0' indicates that the dataset was not used for integration. There are two examples, Edwards et al. [99] (all conditions) and Sorensen et al. [96] (all conditions), where the dataset passed the filter but was not used in the integration. This is because all components in these experiments passed the filter criteria, but to remove redundant data, the subcomponent datasets were taken in favor of the dataset defined over the full set of conditions.