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Referee comments: Referee 2 (Gabor Balazsi)

Posted by PLOS_ONE_Group on 07 Mar 2008 at 10:03 GMT

Referee 2's review (Gabor Balazsi):

In this manuscript, Jupiter and VanBuren 1) present a web-based tool (StarNet) for visualizing cross-correlation based mouse gene networks; 2) compare the distribution of cross-correlation coefficients and genecentric networks for the full dataset and a cardiac cohort.

The manuscript has no major faults, and StarNet might be a useful tool for biologists looking for candidate genes interacting/regulating a gene of interest. I believe the manuscript could be improved if the authors addressed the following comments:

- Some parts of the manuscript are not clear. For example, the Results start off with a sentence about "a genecentric distribution", but such a distribution has not yet been defined. The statistical tests that were used to determine the p-values should be mentioned in parentheses after the p-values. In the Introduction a reference to the source of data should be given. In general, some information from the Methods should appear in the Results too, to make the manuscript clear.
- On page 4, 3' is followed by "prime"
- On page 4, there should be a reference after Dai et al.
- The first reference has a typo in it
- How were the ranges of correlations (indicated by various shades of blue under the network) determined? Was the full range of genecentric correlations equally partitioned?
- It would be interesting to see if the differences observed for the cardiac cohort hold for another tissue-specific subset
- It would be interesting to discuss if the difference between the networks in Fig. 3A and 3B could be somehow quantified.

N.B. These are the comments made by the referee when reviewing an earlier version of this paper. Prior to publication the manuscript has been revised in light of these comments and to address other editorial requirements.