Title: A novel endoplasmic reticulum stress-related lncRNA signature for prognosis prediction
and immune response evaluation in Stomach adenocarcinoma
Version: 0 Date: 24 Sep 2023
Reviewer's report:
Song et.al developed a novel endoplasmic reticulum stress-related lncRNA signature that
predicts STAD prognosis and immune response. Several problems should be addressed before
publication.
1. The classification strategy of training and test sets should be listed in the method section.
Moreover, the results of the manuscript were obtained from only TCGA datasets. It’s necessary
to estimate the efficacy of lncRNA signature in an external validation dataset.
2. In line 111, the sentence ‘We utilized the “limma” R package to quantify the correlation
between lncRNAs and ERS-related genes.’ is not suitable, it seems like the correlation analysis
was performed by limma packages. However, the limma packages only provide DE analysis.
3. From lines 164-174, the immune resource that the authors provided is not correct. The authors
should provide how they get the TIME and immune checkpoint in Figure 7. The sentence
‘Finally, immune checkpoint molecules were evaluated using the “oncoPredict”, “parallel” and
“limma” R packages and visualized by boxplot using “ggplot2” and “ggpubr” R packages.’
Is not suitable, it seems like the authors estimated the immune checkpoint molecules via
“oncoPredict”, “parallel” and “limma”. However, the oncopredict is used to perform drug
response analysis.
4. Current research progress about the relationships between ERS and lncRNAs should be
discussed.
5. Authors should discuss the roles of lncRNAs in cancer immune regulation like PMID:
34654454, 37056564, 28829444...... Besides, the correlation between the 9 ERS-related lncRNA
and TIME or immune checkpoint molecules should be performed.
Title: A novel endoplasmic reticulum stress-related lncRNA signature for prognosis prediction
and immune response evaluation in Stomach adenocarcinoma
Version: 0 Date: 24 Sep 2023
Reviewer's report:
Song et.al developed a novel endoplasmic reticulum stress-related lncRNA signature that
predicts STAD prognosis and immune response. Several problems should be addressed before
publication.
1. The classification strategy of training and test sets should be listed in the method section.
Moreover, the results of the manuscript were obtained from only TCGA datasets. It’s necessary
to estimate the efficacy of lncRNA signature in an external validation dataset.
2. In line 111, the sentence ‘We utilized the “limma” R package to quantify the correlation
between lncRNAs and ERS-related genes.’ is not suitable, it seems like the correlation analysis
was performed by limma packages. However, the limma packages only provide DE analysis.
3. From lines 164-174, the immune resource that the authors provided is not correct. The authors
should provide how they get the TIME and immune checkpoint in Figure 7. The sentence
‘Finally, immune checkpoint molecules were evaluated using the “oncoPredict”, “parallel” and
“limma” R packages and visualized by boxplot using “ggplot2” and “ggpubr” R packages.’
Is not suitable, it seems like the authors estimated the immune checkpoint molecules via
“oncoPredict”, “parallel” and “limma”. However, the oncopredict is used to perform drug
response analysis.
4. Current research progress about the relationships between ERS and lncRNAs should be
discussed.
5. Authors should discuss the roles of lncRNAs in cancer immune regulation like PMID:
34654454, 37056564, 28829444...... Besides, the correlation between the 9 ERS-related lncRNA
and TIME or immune checkpoint molecules should be performed.
Please review this paper.
user
Title: A novel endoplasmic reticulum stress-related lncRNA signature for prognosis prediction
and immune response evaluation in Stomach adenocarcinoma
Version: 0 Date: 24 Sep 2023
Reviewer's report:
Song et.al developed a novel endoplasmic reticulum stress-related lncRNA signature that
predicts STAD prognosis and immune response. Several problems should be addressed before
publication.
1. The classification strategy of training and test sets should be listed in the method section.
Moreover, the results of the manuscript were obtained from only TCGA datasets. It’s necessary
to estimate the efficacy of lncRNA signature in an external validation dataset.
2. In line 111, the sentence ‘We utilized the “limma” R package to quantify the correlation
between lncRNAs and ERS-related genes.’ is not suitable, it seems like the correlation analysis
was performed by limma packages. However, the limma packages only provide DE analysis.
3. From lines 164-174, the immune resource that the authors provided is not correct. The authors
should provide how they get the TIME and immune checkpoint in Figure 7. The sentence
‘Finally, immune checkpoint molecules were evaluated using the “oncoPredict”, “parallel” and
“limma” R packages and visualized by boxplot using “ggplot2” and “ggpubr” R packages.’
Is not suitable, it seems like the authors estimated the immune checkpoint molecules via
“oncoPredict”, “parallel” and “limma”. However, the oncopredict is used to perform drug
response analysis.
4. Current research progress about the relationships between ERS and lncRNAs should be
discussed.
5. Authors should discuss the roles of lncRNAs in cancer immune regulation like PMID:
34654454, 37056564, 28829444...... Besides, the correlation between the 9 ERS-related lncRNA
and TIME or immune checkpoint molecules should be performed.
assistant