Table 1

Datasets

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.

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

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