PONE-D-20-17839

Three novel prognostic biomarkers for seminoma identified by weighted gene coexpression network analysis

PLOS ONE

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Academic Editor

PLOS ONE

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Additional Editor Comments (if provided):

A related work using network modules (PMID: 24075989) should be discussed

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: No

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: No

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: No

Reviewer #2: No

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: The present manuscript titled as “Three novel prognostic biomarkers for seminoma identified by weighted gene coexpression network analysis” used a WGCNA method to analyze seminoma-correlated modules and core genes for identifying prognostic biomarkers for seminoma. Overall, the approach employed in this study is to straightforward and the results are not solid. Below are some comments:

1. “Three novel prognostic biomarkers” is not clear. I suggest to revise it as “Three-gene prognostic biomarkers”.

2. Abstract is not concise enough.

3. Many grammatic errors. English should be improved.

4. Table 1: Why “P value in Survival analysis” and “P value in Univariate Cox analysis” were different? The “P value in Univariate Cox analysis” for TYROBP is not less than 0.05, and the “P value in Survival analysis” for ITGAM is also not less than 0.05. So how to interpret these genes were significantly corelated with survival?

5. The authors claimed the three genes can be used as prognostic biomarker, but no intendent dataset was used for validation. They just analyzed the association of these genes to survival in the TCGA dataset.

Reviewer #2: The author used weighted gene coexpression network analysis and identified three novel prognostic biomarkers for seminoma. I hope the manuscript could be further strengthened by the following comments.

1. Please clearly state the major innovation of this work.

2. More details about the construction of weighted correlation network should be given. How was the correlation matrix constructed and transformed into weighted adjacency matrix? What is the blue and green modules?

3. Please add a flowchart of the construction of weighted correlation network.

4. Please give the reason for parameter selection (e.g., the soft threshold).

5. I want to know whether this network analysis can also be used for the analysis of the other cancers?

6. You should revise your English writing carefully and eliminate small errors in the paper to make the paper easier to understand.

7. Could you discuss the recent trend of developing computational model for identification of the non-coding RNA biomarker of human complex diseases as the future direction of your current research about biomarker identification of seminoma? Some important studies should be cited and discussed (PMIDs: 31927572, 29939227, 29045685, and 24002109).

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Reviewer #1: No

Reviewer #2: No

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Three-gene prognostic biomarkers for seminoma identified by weighted gene co-expression network analysis

PONE-D-20-17839R1

Dear Dr. Chen,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Edwin Wang

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: No

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: Please provide the source code of the analysis in this study publically available, which is necessary for reproducing the results.

Reviewer #2: It could be accepted now

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No