Analysis of ROMO1 Expression Levels and Its Oncogenic Role in Gastrointestinal Tract Cancers

We would like to thank the reviewers for careful and thorough reading of this manuscript and for the thoughtful comments and constructive suggestions, which help to improve the quality of this manuscript. Following your suggestions, we made the necessary corrections to the manuscript to make it better. Our response follows (the reviewer’s comments are in bold).

Comments 1: Correct the problem of joined words in lines 151-153, 164, 201 and 213.

Response 1: Based on your suggestion, the problem with joined words in the lines 151-153, 164, 201 and 213 corrected.

Comments 2: Missing space between words in 246, 249 and 286.

Response 2: We thank the Reviewer for this comment. Space added between words 246, 249, and 286.

Comments 3: No discussion of the results obtained from STRING and GeneMANIAtool to construct the romo1-interacted molecule network. In general, the discussion needs to be restructured, more discussion is needed, there are results that cannot be discussed.

Response 3: • We are grateful for your attention and careful reading. Thank you for this comment and we fully agree with this point. The results obtained from STRING and GeneMANIA tool to construct the ROMO1 interacting molecule network were discussed according to your suggestion. In general, the discussion was restructured. All changes and edits were highlighted in the discussion section of the manuscript.

Response to Reviewer 2 Comments

We would like to thank the reviewers for careful and thorough reading of this manuscript and for the thoughtful comments and constructive suggestions, which help to improve the quality of this manuscript. Following your suggestions, we made the necessary corrections to the manuscript to make it better. Our response follows (the reviewer’s comments are in bold).

Comments 1: The authors present a study that looks to understand the role of ROMO1 in GI cancers. This is an interesting study in my opinion and should be published. I have a few comments

Response 1: We wish to thank the Reviewer for appreciating our work.

Comments 2:  Abstract is concise and well written - could the authgors be more specific about the levels of ROMO1 in different cancers - rather than say significantly increased?

Also could authors be a bit more specific about the clinical utility of these findings or future work to enable this?

Response 2: We thank the Reviewer for this comment. Based on your suggestion, the abstract section was edited and highlighted in the manuscript.

Comments 3: Introduction

The abbreviation to GI doesn't seem to make sense when used as a standalone in sentences i.e. "GI accounts for almost one-third of cancer-related deaths" It maybe makes sense to abbreviate Gastrointestinal Tract cancers, or add the word cancers after GI. There are quite a few instances at the beginning of the introduction? e.g. " GI is estimated to reach 7.5 million new cases

Response 3: • We wish to thank the Reviewer for this constructive comment. We added the word "cancers" after GI to the manuscript. All changes are highlighted in the manuscript.

Comments 4: Some abbreviations given but others not? "NF-κB, ERK, MAPK, 51 p53, and PI3-K.

Response 4: The full name of the abbreviations was added to the manuscript.

Comments 5: needs reference? "The use of bioinformatic analysis to analyze the course of cancer and pinpoint prospective treatment targets has increased significantly in recent years."

Response 5: Based on your suggestion, reference was added to the manuscript

Comments 6: The aims and objectives are not outlined that well "Herein, we used a variety of bioinformatics techniques to investigate romo1 expression profiles, diagnostic value, genetic alteration, protein methylation level, immunological infiltration, and functional states in GI."  could outline the techniques and give more specific details

Response 6: Thank you for this comment and we fully agree with this point. The aim of the study was written in more detail and highlighted in the manuscript.

Comments 7: Methods - not all abbreviations given in this section. Some of the platform names are but some aren't.

Response 7: Full names and abbreviations of all platforms were added to the manuscript

Comments 8: Also I feel that the exact processes undertaken could be outlined. The information is very general?

For example "UALCAN is a fast and effective online analysis and mining website, mainly based on the TCGA database related cancer data, and can provide a large number of comprehensive analysis, including gene expression, survival analysis, and epigenetic regulation [21]. "

I think the whole section could be outlined more clearly in terms of specific processes/setings etc. to facilitate understanding/ replication

Response 8: We are grateful for your valuable contributions. Since there are so many analyses, we tried to summarize the order of the analyses in this way for a better understanding of the method section.

Comments 9: Results

Figure 1 is hard to interpret due to the size

Figure 7 is very difficult to interpret, maybe move to supplementary material?

Figure 8 - I feel the tools are generating a lot of complex diagrams but they are not easy to interpret due to the size/complexity. Could the auhors be more selective in presenting the most significant results.

Response 9: We reduced the size of the figures to fit into the manuscript. Based on your constructive suggestion, we have provided all analyses as supplementary material.

Figure 5 - how is the comparison valid if you have such a small n for normal vs. large n for tumours across the groups?

Comments 10: Is this the case for other analyses? The numbers in Figure 6 are also disproportionate albeit less so.

Response 10: Thank you for this suggestion. Sample numbers are the sample sizes obtained as a result of scanning the database and tools. Unfortunately, we cannot make changes to the sample numbers. The statistical calculations of the analyses are made through this database and tools. The comparison between the groups was calculated according to the sample size obtained as a result of all the database scans.

Comments 11: Discussion - first paragraph of discussion is duplicating part of the introduction and reads like the introduction. It is not contextualizing the results.

Response 11: Based on your constructive and valuable suggestion, we edited the first paragraph of the discussion section and highlighted it in the manuscript.

Comments 12: I think there needs to be more on the limitations of the current work and specifically how to address these

This is not enough "However, the article has some limitations; the role of ROMO1 needs to be experimentally confirmed in vivo and in vitro. Also, larger sample sizes in cancer and healthy groups are needed."

I think the authors should address the issue of disproportionate numbers when undertaking comparisons.

Response 12: We are grateful for your attention and careful reading. Thank you for this comment and we fully agree with this point. The limitation section was revised and emphasized in the manuscript based on your valuable contributions.

Comments 13: Conclusion

Be specific about the features "and closely associated with clinicopathological features"

This is not a very specific closing statement "This might reveal fresh information about the molecular causes of GI and possible treatment targets." Also should be GI cancers?

Response 13: Based on your valuable contributions and suggestions, the results section was revised and emphasized in the manuscript.