Title: A comprehensive computational analysis to explore the importance of SIGLECs in HCC
biology
Version: 5 Date: 17 Aug 2022
Reviewer's report:
"PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses a testable research
question(s) (brief or other article types: is there a clear objective)?
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with technical rigor to allow
confidence in the results?
No - there are minor issues
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Is the current version of this work technically
sound? If not, can revisions be made to make the work technically sound?
Yes - current version is technically sound
PEER REVIEWER COMMENTS:
GENERAL COMMENTS:
The authors have made an effort on revising the manuscript in response to the previous review.
They added specific descriptions and processes of the various data. They also requested a
professional editing service company (Springer Nature Editing) for grammatical correction and
English polishing. Regarding this revision, this reviewer considered it generally appropriate.
Although no novel bioinformatics or computational methods or approaches were developed,
the analysis of several large-scale data sets including TCGA, GEO, and HCCDB provides
reasonably good value of this work.
REQUESTED REVISIONS:
Minor comments
1. The SIGLECs family genes have been studied with regulatory/functional roles in several
cancer types including HCC (e.g., PMID: 35418152). The authors may slightly justify the
significance of the work in the manuscript.
2. The authors need to carefully check the terms and official names. For example:
GSE: Gene expression omnibus -> it should be GEO: Gene Expression Omnibus. GSE is the
data series.
GTEx: Genotype-Tissue Expression Program (Abbreviation), or Genotype-Tissue Expression
(GTEx) Program (line 91) -> GTEx: Genotype-Tissue Expression or Genotype-Tissue
Expression (GTEx) dataset.
3. Gene set enrichment analysis by WebGestalt: did the authors perform multiple test correction
and by what cutoff to set the significance?
4. The authors may pay attention to cite the reference or website at the first place it appeared
in the manuscript. For example, WebGestalt. And cite all those tools/references consistently.
Some are not cited, such as metascape (line 120).
5. Line 224 “Progression-free survival (PFS) was defined as the time interval from diagnosis to
progression.” The authors may check this definition. Typically, it refers to the time from random
assignment in a clinical trial to disease progression or death from any cause.
6. Table 1, column names need to be enhanced. Like “No. of HCC” is misleading. And
expression of p values should be consistent: 2.340e-30 vs. 0.00000153. There is no need to
footnote GSE; if the authors indeed like to do this, use GEO, not GSE."
Title: A comprehensive computational analysis to explore the importance of SIGLECs in HCC
biology
Version: 5 Date: 17 Aug 2022
Reviewer's report:
"PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses a testable research
question(s) (brief or other article types: is there a clear objective)?
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with technical rigor to allow
confidence in the results?
No - there are minor issues
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Is the current version of this work technically
sound? If not, can revisions be made to make the work technically sound?
Yes - current version is technically sound
PEER REVIEWER COMMENTS:
GENERAL COMMENTS:
The authors have made an effort on revising the manuscript in response to the previous review.
They added specific descriptions and processes of the various data. They also requested a
professional editing service company (Springer Nature Editing) for grammatical correction and
English polishing. Regarding this revision, this reviewer considered it generally appropriate.
Although no novel bioinformatics or computational methods or approaches were developed,
the analysis of several large-scale data sets including TCGA, GEO, and HCCDB provides
reasonably good value of this work.
REQUESTED REVISIONS:
Minor comments
1. The SIGLECs family genes have been studied with regulatory/functional roles in several
cancer types including HCC (e.g., PMID: 35418152). The authors may slightly justify the
significance of the work in the manuscript.
2. The authors need to carefully check the terms and official names. For example:
GSE: Gene expression omnibus -> it should be GEO: Gene Expression Omnibus. GSE is the
data series.
GTEx: Genotype-Tissue Expression Program (Abbreviation), or Genotype-Tissue Expression
(GTEx) Program (line 91) -> GTEx: Genotype-Tissue Expression or Genotype-Tissue
Expression (GTEx) dataset.
3. Gene set enrichment analysis by WebGestalt: did the authors perform multiple test correction
and by what cutoff to set the significance?
4. The authors may pay attention to cite the reference or website at the first place it appeared
in the manuscript. For example, WebGestalt. And cite all those tools/references consistently.
Some are not cited, such as metascape (line 120).
5. Line 224 “Progression-free survival (PFS) was defined as the time interval from diagnosis to
progression.” The authors may check this definition. Typically, it refers to the time from random
assignment in a clinical trial to disease progression or death from any cause.
6. Table 1, column names need to be enhanced. Like “No. of HCC” is misleading. And
expression of p values should be consistent: 2.340e-30 vs. 0.00000153. There is no need to
footnote GSE; if the authors indeed like to do this, use GEO, not GSE."
Please review this paper.
user
Title: A comprehensive computational analysis to explore the importance of SIGLECs in HCC
biology
Version: 5 Date: 17 Aug 2022
Reviewer's report:
"PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses a testable research
question(s) (brief or other article types: is there a clear objective)?
Yes - there is a clear objective
DESIGN - Is the current approach (including controls and analysis protocols) appropriate for
the objective?
Yes - the approach is appropriate
EXECUTION - Are the experiments and analyses performed with technical rigor to allow
confidence in the results?
No - there are minor issues
STATISTICS - Is the use of statistics in the manuscript appropriate?
Yes - appropriate statistical analyses have been used in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
Yes - the author's interpretation is reasonable
OVERALL MANUSCRIPT POTENTIAL - Is the current version of this work technically
sound? If not, can revisions be made to make the work technically sound?
Yes - current version is technically sound
PEER REVIEWER COMMENTS:
GENERAL COMMENTS:
The authors have made an effort on revising the manuscript in response to the previous review.
They added specific descriptions and processes of the various data. They also requested a
professional editing service company (Springer Nature Editing) for grammatical correction and
English polishing. Regarding this revision, this reviewer considered it generally appropriate.
Although no novel bioinformatics or computational methods or approaches were developed,
the analysis of several large-scale data sets including TCGA, GEO, and HCCDB provides
reasonably good value of this work.
REQUESTED REVISIONS:
Minor comments
1. The SIGLECs family genes have been studied with regulatory/functional roles in several
cancer types including HCC (e.g., PMID: 35418152). The authors may slightly justify the
significance of the work in the manuscript.
2. The authors need to carefully check the terms and official names. For example:
GSE: Gene expression omnibus -> it should be GEO: Gene Expression Omnibus. GSE is the
data series.
GTEx: Genotype-Tissue Expression Program (Abbreviation), or Genotype-Tissue Expression
(GTEx) Program (line 91) -> GTEx: Genotype-Tissue Expression or Genotype-Tissue
Expression (GTEx) dataset.
3. Gene set enrichment analysis by WebGestalt: did the authors perform multiple test correction
and by what cutoff to set the significance?
4. The authors may pay attention to cite the reference or website at the first place it appeared
in the manuscript. For example, WebGestalt. And cite all those tools/references consistently.
Some are not cited, such as metascape (line 120).
5. Line 224 “Progression-free survival (PFS) was defined as the time interval from diagnosis to
progression.” The authors may check this definition. Typically, it refers to the time from random
assignment in a clinical trial to disease progression or death from any cause.
6. Table 1, column names need to be enhanced. Like “No. of HCC” is misleading. And
expression of p values should be consistent: 2.340e-30 vs. 0.00000153. There is no need to
footnote GSE; if the authors indeed like to do this, use GEO, not GSE."
assistant