Dear Dr Ebbels,

Thank you very much for submitting your manuscript "PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration" 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.

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Christos A. Ouzounis

Academic Editor

PLOS Computational Biology

Pedro Mendes

Section Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

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

Reviewer #1: This is a valuable piece of work, describing a new approach for multi-omic data integration and providing interpretable and explainable predictions from these datasets through the use of pathways. The work is well described and complete. The experiments are well designed with thorough checks and good comparisons.

There are a couple of limitations to this work which could be further discussed.

1. There is a nice experiment comparing the prediction with the pathintegrate approach, all molecules that are mapped to pathways and finally prediction using all molecules whether mapped or not. I would appreciate additional discussion around the effect of having unmapped molecules, what is the potential impact on the prediction, and also how does this limit the discovery of new biology through this type of anlaysis.

2. When discussing multi-omics and missing data, you might want to look into MOFA which can handle missing data rather well in its models.

Reviewer #2: This manuscript proposes a novel framework (PathIntegrate) for integrating multiple blocks/types of omics data. This framework first reduces the data from the molecular to the pathway level before applying MB-multivariate or classification modelling. The Authors report advantages in signal detection (i.e. elucidating information from low effect sizes) and improved interpretability of results. Overall, the research is technically sound and I recommend that it be published. The comments below are suggested improvements and queries.

1. Figure 2 presents a nice visual summary of the framework after the pathway transformation step is complete. It would be helpful for the readers to see this earlier (at the beginning of the Results) and have the pathway transformation step included. That way, the readers can see the whole framework before they start reading about the details.

2. The link to the tutorials and documentation doesn't work (the link appears to be case sensitive). This direct link may not be needed as it is easy to find the tutorials and documentation through the GitHub page. I commend the authors for including a Google Colab tutorial - it is easy to follow.

3. Lines 105-107, the Authors state that one of the challenges of multi-omics integration is the heterogeneity in the number of features profiled. They go on to say that PathIntegrate addresses this challenge in the pathway transformation step. However, the pathway coverage of the different omics blocks will still exhibit heterogeneity (this is partially observed in Figure 4D). Can the Authors please elaborate on how PathIntegrate resolves this challenge?

4. I observed some Methods content in the Results (example paragraph starting at line 153) and some Discussion content in the Results (examples: lines 173, 282, 340). The Authors may wish to review content placement for improved cohesion.

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes: Rachel Cavill

Reviewer #2: No

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References:

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Dear Dr Ebbels,

We are pleased to inform you that your manuscript 'PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration' 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,

Christos A. Ouzounis

Academic Editor

PLOS Computational Biology

Pedro Mendes

Section Editor

PLOS Computational Biology

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Reviewer's Responses to Questions

Comments to the Authors:

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

Reviewer #2: All queries were addressed.

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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

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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: No