Dear Prof. Zeng,

Thank you very much for submitting your manuscript "A probabilistic knowledge graph for target identification" for consideration at PLOS Computational Biology.

As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. In light of the reviews (below this email), we would like to invite the resubmission of a significantly-revised version that takes into account the reviewers' comments.

The reviewers appreciate the focus of the manuscript and commend the authors on providing experimental validation of the results. However, they raise several points that should be addressed to strengthen the paper, related to the data used, confirming results of lower-ranked proteins, and improving the discussion.

We cannot make any decision about publication until we have seen the revised manuscript and your response to the reviewers' comments. Your revised manuscript is also likely to be sent to reviewers for further evaluation.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to the review comments and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out.

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Please prepare and submit your revised manuscript within 60 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email. Please note that revised manuscripts received after the 60-day due date may require evaluation and peer review similar to newly submitted manuscripts.

Thank you again for your submission. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Stacey D. Finley, Ph.D.

Section Editor

PLOS Computational Biology

***********************

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: The review has been uploaded as an attachment.

Reviewer #2: The study introduces Progeni, a machine learning-based framework that integrates heterogeneous biological networks with literature evidence to identify effective drug targets. Progeni's robust predictive power, resilience to exposure bias, and ability to identify target candidates with biological significance in melanoma and colorectal cancer are confirmed through extensive tests and wet-lab experiments, suggesting its potential for improving drug discovery processes. The design of the validation process is sturdy; however, there are numerous major and minor issues that need to be addressed to persuade the reader.

Major issues:

1. Is there a solid rationale for constructing biological networks using outdated resources? The authors utilized DrugBank v3.0, released in 2011, while the most recent version is 5.1.10, published in 2023. Similarly, they used SIDER v3.0 from 2012 instead of the latest version 4.1, released in 2015. With the significant advancements in these fields over the past decade, the constructed networks and prediction results could vary drastically. It is strongly recommended to use the most recent version.

2. The Comparative Toxicogenomics Database contains curated and inferred drug-disease relationships. It's important for the authors to outline which type was used in their study. For accuracy, it is suggested to limit the usage to curated relationships.

3. The authors need to provide a rationale for choosing mouse cell lines over human cell lines for experimental validation, as results from the mouse model may not accurately replicate human outcomes. Furthermore, did the authors limit their calculation of protein-protein co-occurrence frequency to human proteins in the literature? Were orthologs mapped to human proteins? Was mouse protein-protein similarity also considered? To mitigate these potential complications, it is strongly advised to restrict the model to human only.

4. Co-occurrence might not be the most reliable metric for substantiating protein-disease associations, as the correlation could be opposing, i.e., inhibitory or stimulatory. How are these diverse relation types managed within the probabilistic knowledge graph?

5. Only the top-ranked proteins were considered for experimental validation; however, lower-ranked proteins might also be effective in treating melanoma or colorectal cancer. Therefore, it would be advantageous to conduct experiments on some lower-ranked proteins and known treatment targets for melanoma or colorectal cancer as well.

Minor issues:

1. Initially, I found the term "target" perplexing as it typically refers to a drug target in drug discovery studies. The term "biomarker" might be more intuitive, or alternatively, it may be clearer to refer to it as a "disease target" or "treatment target".

2. Which substitution matrix was applied when assessing protein-protein sequence similarity?

3. The arrangement of subfigures (the sequence of a, b, c, and d) in Figure 4 differs from the layout observed in Figures 2 and 3.

4. How is the high or low expression of genes defined within TCGA?

5. For consistency with Figure 5, it is suggested to present the survival curves for primary colorectal cancer patients from TCGA with high or low expression of ADRA2A and EEF2 in Figure 6, irrespective of the results showing significant differences or not.

**********

Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

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: Yes: Liang-Chin Huang

Figure Files:

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

Attachments

Attachment

Submitted filename: PCOMBIOL-D-23-00810 Reviewers comments.docx

Dear Prof. Zeng,

Thank you very much for submitting your manuscript "A probabilistic knowledge graph for target identification" for consideration at PLOS Computational Biology. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

While many reviewer comments have been addressed, some issues remain. The authors are advised to edit the manuscript text to address the remaining concerns, which are centered around validation of the findings. Additional analyses can be included. Additionally, the Discussion can be revised to better reflect the conclusions that can be drawn given experimental validation. Furthermore, there are minor comments that should be addressed.

Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Stacey D. Finley, Ph.D.

Section Editor

PLOS Computational Biology

Stacey Finley

Section Editor

PLOS Computational Biology

***********************

A link appears below if there are any accompanying review attachments. If you believe any reviews to be missing, please contact ploscompbiol@plos.org immediately:

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: I have no major comments left, as they all have been adequately addressed. The discussion is mostly what I was looking for, and some of the overfitting issues have been made as small as possible. I enjoy the extra addition to the Github as well.

Reviewer #2: While the authors have addressed the majority of the comments and suggestions put forth by the reviewers, a few questions remain unresolved or unattended to in the Discussion section.

Major issues:

1. While the authors have updated their datasets, furnished new target candidates, and presented them in the supplementary tables, further validation is lacking. I appreciate the fact that experimental validation may require an extended period of time, but I would encourage the authors to analyze the expressions of these candidates in relation to survival probability at the very least. Furthermore, utilizing the newly added relations in the updated datasets as a test set for the existing model could demonstrate the robustness of the methodology employed.

2. I concur that utilizing a mouse model is sufficient for the experimental validation of the predicted targets. Nevertheless, there are still certain issues that either remain unresolved or have not been addressed: when determining the frequency of protein-protein co-occurrence and their similarity, were human or mouse proteins employed in the calculations? Were orthologs, not just those of the mouse, but others as well, mapped to human proteins?

3. I again recognize that experimental validation could be a lengthy process, however, certain methods such as survival analyses are necessary to justify the relevance of low-ranked proteins. The authors have asserted that "low-ranking proteins will have near-0 correlations, and thus have low relevance to the disease". Without proper validation, this assertion could be questionable since these low-ranking proteins might indeed have significant relevance to the diseases.

4. None of the experimental evidence (such as the images of clones) has been attached.

Minor issue:

The figures and tables are missing titles and captions.

**********

Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

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: Yes: Brandon J. Bongers

Reviewer #2: Yes: Liang-Chin Huang

Figure Files:

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

References:

Review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript.

If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Dear Prof. Zeng,

Thank you very much for submitting your manuscript "A probabilistic knowledge graph for target identification" for consideration at PLOS Computational Biology. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

The reviewers appreciate the revised manuscript. The remaining outstanding action item is to provide the experimental images from which the optical density values were taken. These can be added to the supplementary material and will enhance the rigor and reproducibility of the work.

Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Stacey D. Finley, Ph.D.

Section Editor

PLOS Computational Biology

Stacey Finley

Section Editor

PLOS Computational Biology

***********************

A link appears below if there are any accompanying review attachments. If you believe any reviews to be missing, please contact ploscompbiol@plos.org immediately:

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #2: The authors have solved all the issues and provided supporting evidences.

**********

Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

**********

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 #2: Yes: Liang-Chin Huang

Figure Files:

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

References:

Review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript.

If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

Dear Prof. Zeng,

We are pleased to inform you that your manuscript 'A probabilistic knowledge graph for target identification' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Stacey D. Finley, Ph.D.

Section Editor

PLOS Computational Biology

Stacey Finley

Section Editor

PLOS Computational Biology

***********************************************************