Table 1 |
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|
Datasets |
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|
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 |
|
|
||||
|
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. |
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|
Costello et al. Genome Biology 2009 10:R97 doi:10.1186/gb-2009-10-9-r97 |
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