Title: LINC00634 is a novel prognostic biomarker for colon cancer associated with immune
infiltration
Version: 3 Date: 12 Jul 2024
Reviewer's report:
PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses one or several
testable research questions? (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 sufficient technical rigor to
allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
No - there are issues with the statistics in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
No - there are minor issues
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: The authors responded to my comments and made some changes
to the manuscript. The changes improved the manuscript. However, the authors chose not to
revise the manuscript based on some comments. In particular, the authors did not include a
table of clinical and demographic characteristics, stating: “We would like to inform you that our
study utilizes data from The Cancer Genome Atlas (TCGA) dataset. Unfortunately, the TCGA
dataset does not include comprehensive information on all demographic, clinical, and treatment
variables that you mentioned.” This statement is inconsistent with the nomogram and regression
that used age, gender and TNM, which are clinical and demographic variables. I tried to find
the 455 tumors extracted in the TCGA to validate the findings but was unable to reproduce the
cohort exactly. The authors should give readers more information about how they can find the
455 specimens. In this way, readers can reproduce and extract relevant information (such as age,
gender, and TNM descriptive statistics) even if the authors do not provide that information.
REQUESTED REVISIONS:
Comment 1: The response suggests that some variables used in Figure 4 are not available in the
TCGA data. I tried to access the data to confirm whether the variables did or did not exist, but
I could not find the exact participant data in the TCGA. To help with reproducibility, it would
be useful for the authors to provide more detailed information that would direct readers to the
exact location in the database where the 455 colon tumor samples exist. This may include a
supplement with the sample or participant IDs, or a more specific description of how the data
was extracted from the TCGA such that others could extract the same data.
Comment 2: Some of the numbers are not consistent with a sample size of 455. For example, in
the caption for Figure 3, the authors have a total n of 454.
ADDITIONAL REQUESTS/SUGGESTIONS:
I have no further comments.
Title: LINC00634 is a novel prognostic biomarker for colon cancer associated with immune
infiltration
Version: 3 Date: 12 Jul 2024
Reviewer's report:
PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses one or several
testable research questions? (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 sufficient technical rigor to
allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
No - there are issues with the statistics in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
No - there are minor issues
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: The authors responded to my comments and made some changes
to the manuscript. The changes improved the manuscript. However, the authors chose not to
revise the manuscript based on some comments. In particular, the authors did not include a
table of clinical and demographic characteristics, stating: “We would like to inform you that our
study utilizes data from The Cancer Genome Atlas (TCGA) dataset. Unfortunately, the TCGA
dataset does not include comprehensive information on all demographic, clinical, and treatment
variables that you mentioned.” This statement is inconsistent with the nomogram and regression
that used age, gender and TNM, which are clinical and demographic variables. I tried to find
the 455 tumors extracted in the TCGA to validate the findings but was unable to reproduce the
cohort exactly. The authors should give readers more information about how they can find the
455 specimens. In this way, readers can reproduce and extract relevant information (such as age,
gender, and TNM descriptive statistics) even if the authors do not provide that information.
REQUESTED REVISIONS:
Comment 1: The response suggests that some variables used in Figure 4 are not available in the
TCGA data. I tried to access the data to confirm whether the variables did or did not exist, but
I could not find the exact participant data in the TCGA. To help with reproducibility, it would
be useful for the authors to provide more detailed information that would direct readers to the
exact location in the database where the 455 colon tumor samples exist. This may include a
supplement with the sample or participant IDs, or a more specific description of how the data
was extracted from the TCGA such that others could extract the same data.
Comment 2: Some of the numbers are not consistent with a sample size of 455. For example, in
the caption for Figure 3, the authors have a total n of 454.
ADDITIONAL REQUESTS/SUGGESTIONS:
I have no further comments.
Please review this paper.
user
Title: LINC00634 is a novel prognostic biomarker for colon cancer associated with immune
infiltration
Version: 3 Date: 12 Jul 2024
Reviewer's report:
PEER REVIEWER ASSESSMENTS:
OBJECTIVE - Full research articles: is there a clear objective that addresses one or several
testable research questions? (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 sufficient technical rigor to
allow confidence in the results?
Yes - experiments and analyses were performed appropriately
STATISTICS - Is the use of statistics in the manuscript appropriate?
No - there are issues with the statistics in the study
INTERPRETATION - Is the current interpretation/discussion of the results reasonable and not
overstated?
No - there are minor issues
OVERALL MANUSCRIPT POTENTIAL - Has the author addressed your concerns sufficiently
for you to now recommend the work as a technically sound contribution? If not, can further
revisions be made to make the work technically sound?
Probably - with minor revisions
PEER REVIEWER COMMENTS:
GENERAL COMMENTS: The authors responded to my comments and made some changes
to the manuscript. The changes improved the manuscript. However, the authors chose not to
revise the manuscript based on some comments. In particular, the authors did not include a
table of clinical and demographic characteristics, stating: “We would like to inform you that our
study utilizes data from The Cancer Genome Atlas (TCGA) dataset. Unfortunately, the TCGA
dataset does not include comprehensive information on all demographic, clinical, and treatment
variables that you mentioned.” This statement is inconsistent with the nomogram and regression
that used age, gender and TNM, which are clinical and demographic variables. I tried to find
the 455 tumors extracted in the TCGA to validate the findings but was unable to reproduce the
cohort exactly. The authors should give readers more information about how they can find the
455 specimens. In this way, readers can reproduce and extract relevant information (such as age,
gender, and TNM descriptive statistics) even if the authors do not provide that information.
REQUESTED REVISIONS:
Comment 1: The response suggests that some variables used in Figure 4 are not available in the
TCGA data. I tried to access the data to confirm whether the variables did or did not exist, but
I could not find the exact participant data in the TCGA. To help with reproducibility, it would
be useful for the authors to provide more detailed information that would direct readers to the
exact location in the database where the 455 colon tumor samples exist. This may include a
supplement with the sample or participant IDs, or a more specific description of how the data
was extracted from the TCGA such that others could extract the same data.
Comment 2: Some of the numbers are not consistent with a sample size of 455. For example, in
the caption for Figure 3, the authors have a total n of 454.
ADDITIONAL REQUESTS/SUGGESTIONS:
I have no further comments.
assistant