Reviewer’ s report
Title: Transcriptomic analysis on the effects of melatonin in gastrointestinal carcinomas
Version: 0Date: 14 Apr 2020
Reviewer: Meng Zhou
Reviewer's report:
The manuscript titled "Transcriptomic analysis on the effects of melatonin in gastrointestinal
carcinomas" by Ao L et al., investigated preclinically how melatonin influences expression levelsof several genes and biological pathways commonly altered in gastrointestinal carcinomas and/orinvolved in the development of drug resistance. The manuscript contains a set of novel valuabledata, well written and easy to follow. The bioinformatics analyses in this study appeared robustand logical. The results are all very interesting. However, there are some points that should beaddressed:1. Why Authors use two different methods: students' t-test and PD, to detect DEGs betweentreated and control groups. How to combine the different DEGs lists from different methods? Theyshould state clearly in the section of methods.2. The section "Reproducibility evaluation of two DEG lists" seems not to be relevant in themanuscript. They may delete the part or explain how to use the reproducibility evaluation.3. Authors should add a discussion about DEGs influenced by melatonin in the protein-proteininteraction network, their functions and relationships with genes related to 5-FU resistance.Besides, the experiments and results were observed in cell lines and they also should add thediscussion from in vitro to in vivo, which will increase the significance of the manuscript.
Minor language editing is needed, e.g., the gene symbol should be italic, and the following
sentences: "Gene expression profiling provides an opportunity for researchers to investigate thesepotential effects of melatonin systematically on cancer development and therapeutic response."
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
YesDoes the work include the necessary controls?
If not, please specify which controls are required in your comments to the authors.
YesAre the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
Yes
Are you able to assess any statistics in the manuscript or would you recommend an
additional statistical review?If an additional statistical review is recommended, please specify what aspects require furtherassessment in your comments to the editors.
I am able to assess the statisticsQuality of written English
Please indicate the quality of language in the manuscript:
Needs some language corrections before being published
Declaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of thismanuscript, either now or in the future?
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?
4. Have you received reimbursements, fees, funding, or salary from an organization that holds
or has applied for patents relating to the content of the manuscript?
5. Do you have any other financial competing interests?
6. Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests' below.
If your reply is yes to any, please give details below.
I declare that I have no competing interestsI agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named reportincluding any attachments I upload will be posted on the website along with the authors'responses. I agree for my report to be made available under an Open Access Creative CommonsCC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any commentswhich I do not wish to be included in my named report can be included as confidential commentsto the editors, which will not be published.
I agree to the open peer review policy of the journal
Reviewer’ s report
Title: Transcriptomic analysis on the effects of melatonin in gastrointestinal carcinomas
Version: 0Date: 14 Apr 2020
Reviewer: Meng Zhou
Reviewer's report:
The manuscript titled "Transcriptomic analysis on the effects of melatonin in gastrointestinal
carcinomas" by Ao L et al., investigated preclinically how melatonin influences expression levelsof several genes and biological pathways commonly altered in gastrointestinal carcinomas and/orinvolved in the development of drug resistance. The manuscript contains a set of novel valuabledata, well written and easy to follow. The bioinformatics analyses in this study appeared robustand logical. The results are all very interesting. However, there are some points that should beaddressed:1. Why Authors use two different methods: students' t-test and PD, to detect DEGs betweentreated and control groups. How to combine the different DEGs lists from different methods? Theyshould state clearly in the section of methods.2. The section "Reproducibility evaluation of two DEG lists" seems not to be relevant in themanuscript. They may delete the part or explain how to use the reproducibility evaluation.3. Authors should add a discussion about DEGs influenced by melatonin in the protein-proteininteraction network, their functions and relationships with genes related to 5-FU resistance.Besides, the experiments and results were observed in cell lines and they also should add thediscussion from in vitro to in vivo, which will increase the significance of the manuscript.
Minor language editing is needed, e.g., the gene symbol should be italic, and the following
sentences: "Gene expression profiling provides an opportunity for researchers to investigate thesepotential effects of melatonin systematically on cancer development and therapeutic response."
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
YesDoes the work include the necessary controls?
If not, please specify which controls are required in your comments to the authors.
YesAre the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
Yes
Are you able to assess any statistics in the manuscript or would you recommend an
additional statistical review?If an additional statistical review is recommended, please specify what aspects require furtherassessment in your comments to the editors.
I am able to assess the statisticsQuality of written English
Please indicate the quality of language in the manuscript:
Needs some language corrections before being published
Declaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of thismanuscript, either now or in the future?
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?
4. Have you received reimbursements, fees, funding, or salary from an organization that holds
or has applied for patents relating to the content of the manuscript?
5. Do you have any other financial competing interests?
6. Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests' below.
If your reply is yes to any, please give details below.
I declare that I have no competing interestsI agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named reportincluding any attachments I upload will be posted on the website along with the authors'responses. I agree for my report to be made available under an Open Access Creative CommonsCC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any commentswhich I do not wish to be included in my named report can be included as confidential commentsto the editors, which will not be published.
I agree to the open peer review policy of the journal
Please review this paper.
user
Reviewer’ s report
Title: Transcriptomic analysis on the effects of melatonin in gastrointestinal carcinomas
Version: 0Date: 14 Apr 2020
Reviewer: Meng Zhou
Reviewer's report:
The manuscript titled "Transcriptomic analysis on the effects of melatonin in gastrointestinal
carcinomas" by Ao L et al., investigated preclinically how melatonin influences expression levelsof several genes and biological pathways commonly altered in gastrointestinal carcinomas and/orinvolved in the development of drug resistance. The manuscript contains a set of novel valuabledata, well written and easy to follow. The bioinformatics analyses in this study appeared robustand logical. The results are all very interesting. However, there are some points that should beaddressed:1. Why Authors use two different methods: students' t-test and PD, to detect DEGs betweentreated and control groups. How to combine the different DEGs lists from different methods? Theyshould state clearly in the section of methods.2. The section "Reproducibility evaluation of two DEG lists" seems not to be relevant in themanuscript. They may delete the part or explain how to use the reproducibility evaluation.3. Authors should add a discussion about DEGs influenced by melatonin in the protein-proteininteraction network, their functions and relationships with genes related to 5-FU resistance.Besides, the experiments and results were observed in cell lines and they also should add thediscussion from in vitro to in vivo, which will increase the significance of the manuscript.
Minor language editing is needed, e.g., the gene symbol should be italic, and the following
sentences: "Gene expression profiling provides an opportunity for researchers to investigate thesepotential effects of melatonin systematically on cancer development and therapeutic response."
Are the methods appropriate and well described?
If not, please specify what is required in your comments to the authors.
YesDoes the work include the necessary controls?
If not, please specify which controls are required in your comments to the authors.
YesAre the conclusions drawn adequately supported by the data shown?
If not, please explain in your comments to the authors.
Yes
Are you able to assess any statistics in the manuscript or would you recommend an
additional statistical review?If an additional statistical review is recommended, please specify what aspects require furtherassessment in your comments to the editors.
I am able to assess the statisticsQuality of written English
Please indicate the quality of language in the manuscript:
Needs some language corrections before being published
Declaration of competing interests
Please complete a declaration of competing interests, considering the following questions:
1. Have you in the past five years received reimbursements, fees, funding, or salary from an
organisation that may in any way gain or lose financially from the publication of thismanuscript, either now or in the future?
2. Do you hold any stocks or shares in an organisation that may in any way gain or lose
financially from the publication of this manuscript, either now or in the future?
3. Do you hold or are you currently applying for any patents relating to the content of the
manuscript?
4. Have you received reimbursements, fees, funding, or salary from an organization that holds
or has applied for patents relating to the content of the manuscript?
5. Do you have any other financial competing interests?
6. Do you have any non-financial competing interests in relation to this paper?
If you can answer no to all of the above, write 'I declare that I have no competing interests' below.
If your reply is yes to any, please give details below.
I declare that I have no competing interestsI agree to the open peer review policy of the journal. I understand that my name will be included
on my report to the authors and, if the manuscript is accepted for publication, my named reportincluding any attachments I upload will be posted on the website along with the authors'responses. I agree for my report to be made available under an Open Access Creative CommonsCC-BY license (http://creativecommons.org/licenses/by/4.0/). I understand that any commentswhich I do not wish to be included in my named report can be included as confidential commentsto the editors, which will not be published.
I agree to the open peer review policy of the journal
assistant