Title: The expression of SERPINE1 in colon cancer and its regulatory network and prognostic
value
Version: 2 Date: 18 Jul 2022
Reviewer's report:
The manuscript  by Wang et al. aims to analyse gene expression and patient survival associated
with SERPINE1 expression in colorectal cancer, using different databases.
While the approach is good, there are several shortcomings in the manuscript.
1. In Fig 3A, B and D, the normal (control) samples (n=41) should also be stratified according
to patient's age, gender, race, and compare the COAD samples with the corresponding controls.
The statistical analysis of  the data in Fig 3 is not correct. Instead of t-tests, one-way ANOVA
(or the non-parametric equivalent) should be carried out.
2. In Fig 5B and C, it is not quite clear what the colour codes indicate. In the legend to Fig 6, it
should be clarified what the number of leading-edge genes refer to.
3. In Fig  7, clarification is needed  whether SERPINE1 is regulated by those kinases, miRNA
and transcription factors, or the other way around.
4. In general, the figure legends are very  simplistic,  lacking information of  how the analysis
was done and what the graphs actually show. The statistical analysis performed should also be
added to each figure legend.
5. The formatting of the figures is inconsistent, e.g. Fig 2A vs. B, and Fig 4A,B,C vs. D,E,F.
The formatting of the figures should be consistent throughout.
6. A more extended list of abbreviations is needed. The symbols for genes should be italicized.
7. The title of the manuscript should be amended to refer to the overall survival data (prognostic
value of SERPINE1) too. The manuscript would also benefit from better explanation of the
methods and the results.
Title: The expression of SERPINE1 in colon cancer and its regulatory network and prognostic
value
Version: 2 Date: 18 Jul 2022
Reviewer's report:
The manuscript  by Wang et al. aims to analyse gene expression and patient survival associated
with SERPINE1 expression in colorectal cancer, using different databases.
While the approach is good, there are several shortcomings in the manuscript.
1. In Fig 3A, B and D, the normal (control) samples (n=41) should also be stratified according
to patient's age, gender, race, and compare the COAD samples with the corresponding controls.
The statistical analysis of  the data in Fig 3 is not correct. Instead of t-tests, one-way ANOVA
(or the non-parametric equivalent) should be carried out.
2. In Fig 5B and C, it is not quite clear what the colour codes indicate. In the legend to Fig 6, it
should be clarified what the number of leading-edge genes refer to.
3. In Fig  7, clarification is needed  whether SERPINE1 is regulated by those kinases, miRNA
and transcription factors, or the other way around.
4. In general, the figure legends are very  simplistic,  lacking information of  how the analysis
was done and what the graphs actually show. The statistical analysis performed should also be
added to each figure legend.
5. The formatting of the figures is inconsistent, e.g. Fig 2A vs. B, and Fig 4A,B,C vs. D,E,F.
The formatting of the figures should be consistent throughout.
6. A more extended list of abbreviations is needed. The symbols for genes should be italicized.
7. The title of the manuscript should be amended to refer to the overall survival data (prognostic
value of SERPINE1) too. The manuscript would also benefit from better explanation of the
methods and the results.
Please review this paper.
user
Title: The expression of SERPINE1 in colon cancer and its regulatory network and prognostic
value
Version: 2 Date: 18 Jul 2022
Reviewer's report:
The manuscript  by Wang et al. aims to analyse gene expression and patient survival associated
with SERPINE1 expression in colorectal cancer, using different databases.
While the approach is good, there are several shortcomings in the manuscript.
1. In Fig 3A, B and D, the normal (control) samples (n=41) should also be stratified according
to patient's age, gender, race, and compare the COAD samples with the corresponding controls.
The statistical analysis of  the data in Fig 3 is not correct. Instead of t-tests, one-way ANOVA
(or the non-parametric equivalent) should be carried out.
2. In Fig 5B and C, it is not quite clear what the colour codes indicate. In the legend to Fig 6, it
should be clarified what the number of leading-edge genes refer to.
3. In Fig  7, clarification is needed  whether SERPINE1 is regulated by those kinases, miRNA
and transcription factors, or the other way around.
4. In general, the figure legends are very  simplistic,  lacking information of  how the analysis
was done and what the graphs actually show. The statistical analysis performed should also be
added to each figure legend.
5. The formatting of the figures is inconsistent, e.g. Fig 2A vs. B, and Fig 4A,B,C vs. D,E,F.
The formatting of the figures should be consistent throughout.
6. A more extended list of abbreviations is needed. The symbols for genes should be italicized.
7. The title of the manuscript should be amended to refer to the overall survival data (prognostic
value of SERPINE1) too. The manuscript would also benefit from better explanation of the
methods and the results.
assistant