Title: Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal tract defines genes
ontology clusters with tissue expression patterns
Version: 1 Date: 08 Sep 2021
Reviewer's report:
The manuscript entitled ‘Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal
tract defines genes ontology clusters with tissue expression patterns’ presents semantic cluster
analysis of GIT specific E3 ubiquitin ligases for functional classification and ontology
relationships.
The authors attempt to provide an alternative to commonly used ontological analyses. The
manuscript presents a very short or weak background on the topic. The manuscript lacks strong
arguments for conducting this study. But this study is a good attempt to provide alternative
models for functional annotations.  This work can be accepted after addressing few points below:
The manuscript has grammatical errors and authors should thoroughly check the sentence
structures.
1. The literature presented in the manuscript lacks the scientific motivation to support the
requirement of the present study. What is the significant research gap?
2. Line 53-68: This part needs to properly use literature and explain E3 ubiquitin ligases.
3. Why authors choose E3 ubiquitin ligases for this study?
4. Line 73-79: It is a general statement. Need to focus on the why and how it is relevant. What
is the motivation to conduct this study?
5. Line 78: …’ So, this method provides a more complete picture of functional’…. How can you
say that? Any relevant study or research to support the claim?
6. Use recent references to support the literature. Several classical research articles are available
to explain the ubiquitination mechanisms and their components.
7. Many sentences are lacking proper citations and explanations. Authors need to be specific
and the required information in the sentences should be connected.
8. RNA isolation protocol or appropriate reference needed.
9. What E3-Ub ligase genes, internal controls were used in the study?
10. Line 111-119: Use proper reference, protocol, and citation for clear and complete details.
11. Line 121-155: Use proper references to support the methods and procedures.
12. Does this study differentiate any of the classes of the E3 ubiquitin ligases? If not, why?
13. If possible, authors should predict the classes of the E3 ubiquitin ligases of the upregulated
or downregulated genes with structural information.
14. A flow chart showing stepwise details of the semantic cluster analysis would be useful as it
is difficult to follow the text in the methods and results.
15. Line 340-345: Statement is not clear? What do you want to say?
16. Figure 2 is very difficult to read.
17. Provide more explanation for Figure 3 in the manuscript.
18. It is very difficult to follow/read the ‘Additional file’ which has been frequently cited
throughout the manuscript. Authors should better represent the data.
Title: Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal tract defines genes
ontology clusters with tissue expression patterns
Version: 1 Date: 08 Sep 2021
Reviewer's report:
The manuscript entitled ‘Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal
tract defines genes ontology clusters with tissue expression patterns’ presents semantic cluster
analysis of GIT specific E3 ubiquitin ligases for functional classification and ontology
relationships.
The authors attempt to provide an alternative to commonly used ontological analyses. The
manuscript presents a very short or weak background on the topic. The manuscript lacks strong
arguments for conducting this study. But this study is a good attempt to provide alternative
models for functional annotations.  This work can be accepted after addressing few points below:
The manuscript has grammatical errors and authors should thoroughly check the sentence
structures.
1. The literature presented in the manuscript lacks the scientific motivation to support the
requirement of the present study. What is the significant research gap?
2. Line 53-68: This part needs to properly use literature and explain E3 ubiquitin ligases.
3. Why authors choose E3 ubiquitin ligases for this study?
4. Line 73-79: It is a general statement. Need to focus on the why and how it is relevant. What
is the motivation to conduct this study?
5. Line 78: …’ So, this method provides a more complete picture of functional’…. How can you
say that? Any relevant study or research to support the claim?
6. Use recent references to support the literature. Several classical research articles are available
to explain the ubiquitination mechanisms and their components.
7. Many sentences are lacking proper citations and explanations. Authors need to be specific
and the required information in the sentences should be connected.
8. RNA isolation protocol or appropriate reference needed.
9. What E3-Ub ligase genes, internal controls were used in the study?
10. Line 111-119: Use proper reference, protocol, and citation for clear and complete details.
11. Line 121-155: Use proper references to support the methods and procedures.
12. Does this study differentiate any of the classes of the E3 ubiquitin ligases? If not, why?
13. If possible, authors should predict the classes of the E3 ubiquitin ligases of the upregulated
or downregulated genes with structural information.
14. A flow chart showing stepwise details of the semantic cluster analysis would be useful as it
is difficult to follow the text in the methods and results.
15. Line 340-345: Statement is not clear? What do you want to say?
16. Figure 2 is very difficult to read.
17. Provide more explanation for Figure 3 in the manuscript.
18. It is very difficult to follow/read the ‘Additional file’ which has been frequently cited
throughout the manuscript. Authors should better represent the data.
Please review this paper.
user
Title: Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal tract defines genes
ontology clusters with tissue expression patterns
Version: 1 Date: 08 Sep 2021
Reviewer's report:
The manuscript entitled ‘Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal
tract defines genes ontology clusters with tissue expression patterns’ presents semantic cluster
analysis of GIT specific E3 ubiquitin ligases for functional classification and ontology
relationships.
The authors attempt to provide an alternative to commonly used ontological analyses. The
manuscript presents a very short or weak background on the topic. The manuscript lacks strong
arguments for conducting this study. But this study is a good attempt to provide alternative
models for functional annotations.  This work can be accepted after addressing few points below:
The manuscript has grammatical errors and authors should thoroughly check the sentence
structures.
1. The literature presented in the manuscript lacks the scientific motivation to support the
requirement of the present study. What is the significant research gap?
2. Line 53-68: This part needs to properly use literature and explain E3 ubiquitin ligases.
3. Why authors choose E3 ubiquitin ligases for this study?
4. Line 73-79: It is a general statement. Need to focus on the why and how it is relevant. What
is the motivation to conduct this study?
5. Line 78: …’ So, this method provides a more complete picture of functional’…. How can you
say that? Any relevant study or research to support the claim?
6. Use recent references to support the literature. Several classical research articles are available
to explain the ubiquitination mechanisms and their components.
7. Many sentences are lacking proper citations and explanations. Authors need to be specific
and the required information in the sentences should be connected.
8. RNA isolation protocol or appropriate reference needed.
9. What E3-Ub ligase genes, internal controls were used in the study?
10. Line 111-119: Use proper reference, protocol, and citation for clear and complete details.
11. Line 121-155: Use proper references to support the methods and procedures.
12. Does this study differentiate any of the classes of the E3 ubiquitin ligases? If not, why?
13. If possible, authors should predict the classes of the E3 ubiquitin ligases of the upregulated
or downregulated genes with structural information.
14. A flow chart showing stepwise details of the semantic cluster analysis would be useful as it
is difficult to follow the text in the methods and results.
15. Line 340-345: Statement is not clear? What do you want to say?
16. Figure 2 is very difficult to read.
17. Provide more explanation for Figure 3 in the manuscript.
18. It is very difficult to follow/read the ‘Additional file’ which has been frequently cited
throughout the manuscript. Authors should better represent the data.
assistant