Title: Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal tract defines genes
ontology clusters with tissue expression patterns
Version: 1 Date: 13 Sep 2021
Reviewer's report:
In this manuscript, Iatsiuk et al reported their story about tissue specific gene expression patterns
of ubiquitin ligases in murine gastrointestinal tract (GIT) using a semantic clustering analysis
method. The authors also employed a dextran sulfate sodium (DSS) mouse model to survey cell-
type specific distribution changes of certain ubiquitin ligases. Overall, this is a pretty good story,
since there are some studies of this kind using cell lines, but not at animal level. The authors
basically focused on GIT and provided some valuable data for tissue-specific expression patterns
of ubiquitin ligases, especially in GIT. However, one major disappointment is that the whole
study was based on RNA analysis only. It would be much better to incorporate some verification
data of protein expression for certain ubiquitin ligases using western blots or IHC methods.
Minor concerns:
1. APC2 is one subunit of the APC/C ubiquitin ligase. Therefore, it makes no sense to only
examine one subunit of such a big complex of ubiquitin ligase.
2. BRCC3 (also called BRCC36) is a deubiquitination enzyme, but not ubiquitin ligase.
3. There is a typo in Line 301: Don’t know what is “lexpression”?
Title: Semantic clustering analysis of E3-ubiquitin ligases in gastrointestinal tract defines genes
ontology clusters with tissue expression patterns
Version: 1 Date: 13 Sep 2021
Reviewer's report:
In this manuscript, Iatsiuk et al reported their story about tissue specific gene expression patterns
of ubiquitin ligases in murine gastrointestinal tract (GIT) using a semantic clustering analysis
method. The authors also employed a dextran sulfate sodium (DSS) mouse model to survey cell-
type specific distribution changes of certain ubiquitin ligases. Overall, this is a pretty good story,
since there are some studies of this kind using cell lines, but not at animal level. The authors
basically focused on GIT and provided some valuable data for tissue-specific expression patterns
of ubiquitin ligases, especially in GIT. However, one major disappointment is that the whole
study was based on RNA analysis only. It would be much better to incorporate some verification
data of protein expression for certain ubiquitin ligases using western blots or IHC methods.
Minor concerns:
1. APC2 is one subunit of the APC/C ubiquitin ligase. Therefore, it makes no sense to only
examine one subunit of such a big complex of ubiquitin ligase.
2. BRCC3 (also called BRCC36) is a deubiquitination enzyme, but not ubiquitin ligase.
3. There is a typo in Line 301: Don’t know what is “lexpression”?
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: 13 Sep 2021
Reviewer's report:
In this manuscript, Iatsiuk et al reported their story about tissue specific gene expression patterns
of ubiquitin ligases in murine gastrointestinal tract (GIT) using a semantic clustering analysis
method. The authors also employed a dextran sulfate sodium (DSS) mouse model to survey cell-
type specific distribution changes of certain ubiquitin ligases. Overall, this is a pretty good story,
since there are some studies of this kind using cell lines, but not at animal level. The authors
basically focused on GIT and provided some valuable data for tissue-specific expression patterns
of ubiquitin ligases, especially in GIT. However, one major disappointment is that the whole
study was based on RNA analysis only. It would be much better to incorporate some verification
data of protein expression for certain ubiquitin ligases using western blots or IHC methods.
Minor concerns:
1. APC2 is one subunit of the APC/C ubiquitin ligase. Therefore, it makes no sense to only
examine one subunit of such a big complex of ubiquitin ligase.
2. BRCC3 (also called BRCC36) is a deubiquitination enzyme, but not ubiquitin ligase.
3. There is a typo in Line 301: Don’t know what is “lexpression”?
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