Title: Characterization of TGF#-associated molecular features and drug responses in
gastrointestinal adenocarcinoma
Version: 4 Date: 25 Feb 2021
Reviewer:  Genwen Chen
Reviewer's report:
The study by Zhang et al. analyzed the TGF#-associated molecular features in GIAD. They
revealed comprehensive networks of TGF#-associated mRNAs, miRNAs, and proteins. Overall,
the manuscript is well organized but with little novelty, because the TGFb pathway was well-
known and widely studied. There are a number of issues with the manuscript as it stands:
1. Fig. S1: For panels B-E, please consider to indicate cancer types.
2. How and why the authors choose 39 core TGF-# genes. There are many TGF# associated
genes and TGF# signatures. Please discuss the difference with others.
3. The TGF#-associated signatures of STAD was quiet difference from others. Please discuss
about it.
4. How the authors defined TGF# specific expressing miRNAs? It is not clearly explained.
5. In Figure 4B, the heatmap shows the most significantly down-regulated 20 miRNAs in the
TGF#¬¬high group. However, the legend indicated LogFC. Please clarify it.
6. Why the authors used Pearson correlation for all analysis of correlation? Do they all meet the
requirements of Pearson correlation coefficient?
7. Please correct several grammatical errors.
Title: Characterization of TGF#-associated molecular features and drug responses in
gastrointestinal adenocarcinoma
Version: 4 Date: 25 Feb 2021
Reviewer:  Genwen Chen
Reviewer's report:
The study by Zhang et al. analyzed the TGF#-associated molecular features in GIAD. They
revealed comprehensive networks of TGF#-associated mRNAs, miRNAs, and proteins. Overall,
the manuscript is well organized but with little novelty, because the TGFb pathway was well-
known and widely studied. There are a number of issues with the manuscript as it stands:
1. Fig. S1: For panels B-E, please consider to indicate cancer types.
2. How and why the authors choose 39 core TGF-# genes. There are many TGF# associated
genes and TGF# signatures. Please discuss the difference with others.
3. The TGF#-associated signatures of STAD was quiet difference from others. Please discuss
about it.
4. How the authors defined TGF# specific expressing miRNAs? It is not clearly explained.
5. In Figure 4B, the heatmap shows the most significantly down-regulated 20 miRNAs in the
TGF#¬¬high group. However, the legend indicated LogFC. Please clarify it.
6. Why the authors used Pearson correlation for all analysis of correlation? Do they all meet the
requirements of Pearson correlation coefficient?
7. Please correct several grammatical errors.
Please review this paper.
user
Title: Characterization of TGF#-associated molecular features and drug responses in
gastrointestinal adenocarcinoma
Version: 4 Date: 25 Feb 2021
Reviewer:  Genwen Chen
Reviewer's report:
The study by Zhang et al. analyzed the TGF#-associated molecular features in GIAD. They
revealed comprehensive networks of TGF#-associated mRNAs, miRNAs, and proteins. Overall,
the manuscript is well organized but with little novelty, because the TGFb pathway was well-
known and widely studied. There are a number of issues with the manuscript as it stands:
1. Fig. S1: For panels B-E, please consider to indicate cancer types.
2. How and why the authors choose 39 core TGF-# genes. There are many TGF# associated
genes and TGF# signatures. Please discuss the difference with others.
3. The TGF#-associated signatures of STAD was quiet difference from others. Please discuss
about it.
4. How the authors defined TGF# specific expressing miRNAs? It is not clearly explained.
5. In Figure 4B, the heatmap shows the most significantly down-regulated 20 miRNAs in the
TGF#¬¬high group. However, the legend indicated LogFC. Please clarify it.
6. Why the authors used Pearson correlation for all analysis of correlation? Do they all meet the
requirements of Pearson correlation coefficient?
7. Please correct several grammatical errors.
assistant