A. Experimental procedure: cDNA cloning, Yeast two-hybrid, etc.
- The pooling and full genome cloning were not very well explained in the paper.
- Why did authors use two different screenings: cDNA and collection screenings?
- How is the "system bait-prey working?
- what is a draft map?
- Is there any plan to fix the enrichment and depletion of protein classes due to the technical biases of the two-hybrid assay?

B. Generalized Linear Model
- I would also like to understand the math part of this paper.
- How does the automated confidence scoring method work?
- What is a confidence matric?

C. What explanatory variables are used for the generalized linear modeling?

D. How is a generalized linear modeling actually used for the interaction data? (training, etc.)
- It is not clear how the authors calculated the confidence score of two-hybrid interactions in manual and automated training sets?
- why do the authors compare manual annotations with automated annotations for protein interaction modeling?

E. How GO annotations are used to correlate with confidence scores?
- how does one use/interpret GO Gene Ontology annotations/hierarchy?
- How to explain Fig.2 C (the relationship between GO correlation and confidence score)?
- The confidence score of 0.5 used for protein interactions seems to be very high.

F. Statistical test (contingency table, randomization test, etc.) used to identify enriched/depleted protein pairs.
- What is a contingency table ?
- what is Pfam?

G. Scale-free network, small-world network (Fig 2D, Fig 3)
- What is a scale-free network?
- I didn't fully understand the "links" and the mathematical equations for the shortest path between two distinct proteins.

H. How to read Figure 4
- Fig 4A shows different levels of interaction ratings. I would like to know exactly what each level represents?
- It was not clear how the authors arrived at the confidence ratings. In figure four, how many false positives would be expected at each of the different interaction ratings?
- Global views of protein-interaction map in figure 4 are very hard to follow.
- Is there any better way of representing protein-interaction map of figure 4?
- how are the models in figure 4 created, and how do you interpret the lines and shaded regions/groupings?

I. Biological classification used in Figure 4 (Homophila and GO databases, etc.)
- When they compared Drosophila proteins to human disease proteins, how alike did the sequences have to be to be classified as similar?
- Figure 4B shows proteins whose localizations are annotated in the GO database and proteins that have not been annotated previously as well. How was the predicted subcellular localization determined in the case when the protein had several partners localized in different compartments?
- How they classify protein interaction?

J. How can we trust their results?
- Are they working with any labs to confirm or disprove any of the
interesting interactions that they have discovered, in both Drosophila and
other systems?
- I am not sure how reliable their data are. In Fig 5C, they pick out those protein interactions in signal transduction pathway. As we know, signal transduction is regulated in different condition; so those interactions won't exist in all condition. Therefore I doubt your conclusion of signal transduction upon two-hybrid based protein-interaction map.
- What is the result of interaction or association of Slmb with SkpA?