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My comments are addressed by the authors.
My comments are addressed by the authors.
My comments are addressed by the authors.
My comments are addressed by the authors, and the manuscript has been improved a lot.
no comment
no comment
no comment
Authors addressed comments well. I recommend this article be accepted.
Dear authors. Please note the indications of the reviewers. Regards.
[# PeerJ Staff Note: Please ensure that all review and editorial comments are addressed in a response letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. #]
[# PeerJ Staff Note: The review process has identified that the English language must be improved. PeerJ can provide language editing services - please contact us at copyediting@peerj.com for pricing (be sure to provide your manuscript number and title) #]
1 The review of related work is not sufficiently thorough and not sufficiently specific. The authors should cite the latest references if appropriate.
2 Figure 5 needs to be improved.
3 L160-L161 seems not clear. The authors should rephrase it.
1 The authors should add more details in key parts to make the results replicable. For example, what are the gene selection criteria in each database? What is their selection cutoff in each dataset? What are the references they used in PubMed?
2 In fact, the interaction between gene and gene is more complex. I don’t think L104-L105 is a reasonable or robust way to identify key genes or AD-DM2 associations.
3 To my knowledge, there are various filtering criteria to determine PPI in published articles. Is there any reference to support the criteria the authors used (minimum required interaction score>0.9000)? The issues also apply to their PPI hub analysis.
4 The authors should provide information on statistical tests they used throughout the manuscript.
1 The authors should provide the gene lists they filtered in excel file format.
2 The authors should provide the complete lists for Table S4.
3 Most results are more like descriptive reports. The authors should improve them.
4 The Discussion section should be improved to better reflect the quality of the work.
no comment
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This is an interesting study and the authors have mined nine databases to identify information that overlap AD and DM2. gene information was mapped to protein-protein interaction (PPI) networks based on experimental data.gene ontology biological process (GOBP), and pathway analysis accomplished.The authors found that the pathway information for DM2 and the association AD-DM2 were linked mainly to inflammatory alterations. 10 hub proteins were identified, and seven were predicted to be present in plasma.
It is a very interesting work. However, some major concerns should be addressed:
Abstract
- background, clarify the aim of this study.
- conclusion, Please focus the abstract on your study and your results.
Methods
- line 131, “Only proteins with p <0.05 were considered significant, taking only the 10 most significant proteins for each study group (AD, DM2, and AD DM2 association).” Why only top 10, please provide more literature support. And please demonstrate the number of all significant proteins if possible.
Result
- Line 158, “PPI manages important biological processes, including metabolism control (Rao et al., 2014).” That sentence should be in Methods.
Discussion
- “ESR1 is an estrogenic receptor with risk polymorphisms for AD and DM.” ESR1 is at the center of the hub, should be more thoroughly discussed.
Figure 2 & 3 please provide figures with better resolution.
Figure 5 is too complicated. Protein labels could have a smaller font size for better review
Hypothesis is clear but he overall methodology is not sufficiently provided
Figure are of low quality : I find it really difficult to draw any conclusions from the figures .
English need to be improved alot
Experimental section is not explained in detail needs to be improved
Since its an Insilco work , concluding as a major finding is not relevant or seems preliminary
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