Review for 10.1186/s12876-022-02625-y (2023)

Title: The expression of SERPINE1 in colon cancer and its regulatory network and prognostic
value
Version: 4 Date: 18 Nov 2022
Reviewer's report:
My comments on the revised manuscript:
Title
It’s still not ideal, at least SERPINE1 'expression' should be added. Better would be including
‘prognostic value of SERPINE1’.
Abstract
Include that patient survival was also evaluated in association with SERPINE1 expression.
Methods
What analysis was done to obtain the survival curves? This should be included in the Methods
in 1.4 Evaluation of the relationship between SERPINE1 expression and patient survival.
Figures
Fig 2A: An ideal title for the figure would be SERPINE1 expression in COAD samples
(starBase). It would be better to delete all the rest of the words in the figure title.
Also delete ‘Box plot’ and ‘Gene expressions’ from under the X-axis – it’s totally unnecessary,
it’s self-explanatory. The label of the X-axis should be: Normal tissues (n=41) and COAD tissues
(n=471), and show the results of the normal tissues on the left and the cancer tissues on the right
just like in Fig 2B.
Fig 2B: An ideal title for the figure would be Expression of SERPINE1 in COAD samples
(UALCAN); X-axis label: Normal tissues (n=41) and Primary COAD (n=286), and it would be
better to delete ‘TCGA samples’ from under the X-axis.
Fig 3: Needs proper figure legends! A single line of legend is not enough.
Fig 4: The statistical analysis provided (ANOVA) is not suitable for establishing an association
between SERPINE1 expression and the indicated demographic and pathological categories of
colon cancer. Association/correlation tests should be performed.
Fig 5: The type of analysis performed should be indicated in the figure legend. In which criterium
was there a significant difference in the survival of patients with high or low expression of
SERPINE1? – this should be indicated in the figure legend too.
Fig 7: Needs a more extensive figure legend, with more information.
Fig 8: In the figure legend, the phrase ‘targeting related genes’ is odd. It would be better to
rephrase it as ‘targeting genes’ or ‘related genes’.
General
Another round of proofreading of the manuscript would be beneficial.
Just a few examples where rephrasing would be needed:
In the conclusion of the Abstract: ‘Overall, our bioinformatics analyses comprehensively
performed the networks…’ it would be better to change the wording to ‘…comprehensively
described…’
In the last sentence of the Introduction: ‘…which may provide a deeper insight into further
research on the pathogenesis of colon cancer’, it would be better to rephrase it as ‘…as well
as provide a deeper insight into the pathogenesis of colon cancer, which would inform further
research’.
In the last sentence of 2.1 of the Results, instead of ‘Based on the analysis above, we selected
colon cancer that we were interested in, and SERPINE1 expression performed the significant
increase in colon cancer’, it would be better to write ‘Based on the analysis above, we selected
colon cancer in which SERPINE1 was highly expressed.’
Some sentences - e.g., in the Discussion: ‘As only bioinformatics analysis and clinical
experiments in absence of wet experiments for validation, molecular biology experiment
verification is required as an ongoing study process.’ – are not correct grammatically, and
therefore don’t convey the intended message.
A ‘…gene is/was related to…’ is often incorrectly used. In many cases the meaning would have
required to write ‘…a gene is/was interacting or associated with…’