Title: Molecular subtyping based on TRP family and prognostic assessment for TRP-associated
lncRNAs in pancreatic adenocarcinoma
Version: 2 Date: 29 Sep 2022
Reviewer's report:
This article includes a categorisation of pancreatic cancer patients into 3 subgroups based on
TPR-related genes, with a group of patients showing enriched immune signalling. The work also
presents a TPR-associated lncRNA risk signature and its association with immune infiltration
and tumour tissue and cells. The methods used could be applied to other families of proteins.
However, an expanded amount of detail in the description of the results and figure legends would
be beneficial to the reader.
I have the following suggestions for the paper: Throughout the paper, patient tumour samples
are referred to as pancreatic cancer . Although readers could assume that this is referring to
pancreatic ductal adenocarcinoma (PDAC) from the context, it would be more informative to
explicitly mention which pancreatic cancer type is being referred to. The PAAD (pancreatic
adenocarcinoma) TCGA data set includes a small number of non-PDAC samples, if these were
included in the analysis, pancreatic adenocarcinoma should be used to describe the type of
pancreatic cancer described in the work.
Fig.1: It would be preferential if (A) could be done in another format, such as a stacked bar chart
and cBioPortal should be referenced in the text or the figure legend. Additionally, the font of
(D) could be made bigger so that the genes are easily read.
Fig.2: A label in the scale bar or just a comment of what the scale bar represents in the figure
legend is needed for (D) and (E).
Fig.3: (D) would benefit from a better explanation in the text, as it is not fully clear what the
significant differences refer to. If the cut-off statistical value and an explanation of the groups
compared could be included that could avoid confusion.
Fig.8: (D) & (E) PAAD TCGA only has 4 normal samples, the figure would benefit from the
inclusion of GTEx normal pancreas data to increase the n value. This can be done with another
analysis platform (GEPIA).
Title: Molecular subtyping based on TRP family and prognostic assessment for TRP-associated
lncRNAs in pancreatic adenocarcinoma
Version: 2 Date: 29 Sep 2022
Reviewer's report:
This article includes a categorisation of pancreatic cancer patients into 3 subgroups based on
TPR-related genes, with a group of patients showing enriched immune signalling. The work also
presents a TPR-associated lncRNA risk signature and its association with immune infiltration
and tumour tissue and cells. The methods used could be applied to other families of proteins.
However, an expanded amount of detail in the description of the results and figure legends would
be beneficial to the reader.
I have the following suggestions for the paper: Throughout the paper, patient tumour samples
are referred to as pancreatic cancer . Although readers could assume that this is referring to
pancreatic ductal adenocarcinoma (PDAC) from the context, it would be more informative to
explicitly mention which pancreatic cancer type is being referred to. The PAAD (pancreatic
adenocarcinoma) TCGA data set includes a small number of non-PDAC samples, if these were
included in the analysis, pancreatic adenocarcinoma should be used to describe the type of
pancreatic cancer described in the work.
Fig.1: It would be preferential if (A) could be done in another format, such as a stacked bar chart
and cBioPortal should be referenced in the text or the figure legend. Additionally, the font of
(D) could be made bigger so that the genes are easily read.
Fig.2: A label in the scale bar or just a comment of what the scale bar represents in the figure
legend is needed for (D) and (E).
Fig.3: (D) would benefit from a better explanation in the text, as it is not fully clear what the
significant differences refer to. If the cut-off statistical value and an explanation of the groups
compared could be included that could avoid confusion.
Fig.8: (D) & (E) PAAD TCGA only has 4 normal samples, the figure would benefit from the
inclusion of GTEx normal pancreas data to increase the n value. This can be done with another
analysis platform (GEPIA).
Please review this paper.
user
Title: Molecular subtyping based on TRP family and prognostic assessment for TRP-associated
lncRNAs in pancreatic adenocarcinoma
Version: 2 Date: 29 Sep 2022
Reviewer's report:
This article includes a categorisation of pancreatic cancer patients into 3 subgroups based on
TPR-related genes, with a group of patients showing enriched immune signalling. The work also
presents a TPR-associated lncRNA risk signature and its association with immune infiltration
and tumour tissue and cells. The methods used could be applied to other families of proteins.
However, an expanded amount of detail in the description of the results and figure legends would
be beneficial to the reader.
I have the following suggestions for the paper: Throughout the paper, patient tumour samples
are referred to as pancreatic cancer . Although readers could assume that this is referring to
pancreatic ductal adenocarcinoma (PDAC) from the context, it would be more informative to
explicitly mention which pancreatic cancer type is being referred to. The PAAD (pancreatic
adenocarcinoma) TCGA data set includes a small number of non-PDAC samples, if these were
included in the analysis, pancreatic adenocarcinoma should be used to describe the type of
pancreatic cancer described in the work.
Fig.1: It would be preferential if (A) could be done in another format, such as a stacked bar chart
and cBioPortal should be referenced in the text or the figure legend. Additionally, the font of
(D) could be made bigger so that the genes are easily read.
Fig.2: A label in the scale bar or just a comment of what the scale bar represents in the figure
legend is needed for (D) and (E).
Fig.3: (D) would benefit from a better explanation in the text, as it is not fully clear what the
significant differences refer to. If the cut-off statistical value and an explanation of the groups
compared could be included that could avoid confusion.
Fig.8: (D) & (E) PAAD TCGA only has 4 normal samples, the figure would benefit from the
inclusion of GTEx normal pancreas data to increase the n value. This can be done with another
analysis platform (GEPIA).
assistant