Drought Stress-Related Gene Identification in Rice by Random Walk with Restart on Multiplex Biological Networks
Round 1
Reviewer 1 Report
This is an interesting paper based on an interactome (protein-protein and gene coexpression networks) of Rice to identify drought-stress related genes. To achieve this, the authors propose the usage of RWR to further identify candidate genes.
Certainly, this paper benefits from using a novel approach to reduce the number of putative candidate genes obtained by other techniques.
Yet, my biggest concern is that the authors have focused on describing the RWR algorithm procedures (pages 4-5), and I'm not sure if this fits well under the scope of this journal. Thus, it seems that the authors selected Rice as a model species, presumably due to the high amount of data available, but were not quite interested on biological mechanisms of this crop.
This isnt' bad per se, but the discussion is quite brief in terms of the molecular mechanisms involved in drought stress in rice (which, I presume, is important for the readers of this journal as well)
Having said that, I think that the authors should mend some issues before accepting this manuscript:
-Line 36: "which can provide a one time overview of abiotic stress" should mention that authors are interested on molecular mechanisms involved in abiotic stress tolerance/resistance
-Lines 37-46: authors should rephrase to explain the readers that they are proposing to employ a different analysis method, due to the limitations of alternative methods that have been widely used in other studies. Currently the manuscript just states that RWR is an advanced association algorithm just after stating the high demand of computational methods. Then, the authors introduce some concepts as nodes and starting points, which should go below in lines 45-46.
Line 48-50: did the authors use public databases? that should be mentioned briefly in the introduction
Line 58-60: it is unclear why the authors chose that approach. Please explain
Line 60-62: english edition is required here as this sentence is quite hard to read on its current form.
Line 72-75, please rephrase.
Line 72-75: authors must indicate the accession codes for the SRA libraries used in this study (that can be added as supplementary).
line 184: authors do not describe which was the methodology underlying amiGO analysis.
line 192-193: minor corrections are required
line 250-252: I'd rather say that this approach yielded 13 candidates, 5 of which would be actually being involved in drought stress resistance mechanisms, according to the supporting experimental evidence available. I'd be wary of stating that these genes were confirmed, as the authors did not conduct any experiments on these.
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Introduction
Consider moving the last paragraph in introduction to materials and methods section.
Figures 2 and 3, indicate the units on X and Y axis of the graph.
13 candidate genes were identified. However, Authors did not indicate the chromosome location of the identified genes across 12 rice chromosomes.
Authors should check the format of this journal and follow it appropriately.
Chapter 3 line 159 should be Results only and not Results and Discussion
3.7 should be 4.0 Discussion
Extensive editing of English language and style required, preferably, from an expert from a native English speaking country.
Author Response
Please see the attachment.
Author Response File: Author Response.pdf
Round 2
Reviewer 1 Report
The paper has been improved and the authors have replied to all my comments. The usage of these tools is quite interesting, particularly to find related candidate genes. Moreover, authors give some details on the algorithms underlying their analysis.
Hence, I'm accepting the article in its current form
