Title: Characterization of TGF#-associated molecular features and drug responses in
gastrointestinal adenocarcinoma
Version: 6 Date: 15 Apr 2021
Reviewer's report:
1. Regarding the previous question 3: Do you mean that many of the mutations and CNVs in
Fig. 2b lead to loss of function of TGF-b-related genes such as SMAD4? Why does it happen
limited in STAD? The authors should explain it in the main article.
2. Regarding the previous question 4: The authors need to describe how BRAF-V600 inhibitors
affect TGF-b signaling and provide references about it in the main article. It does not mean the
reference should be changed.
3. What is the advantage of using clustering instead of classification by TGF-score in ssGSEA?
Is it because it only requires limited-genes expression data? Is the DNN model useful because
that makes it possible to classify TGF-b subtypes by the only top 10 genes signature? I suggest
that the authors make these points more clear to improve the article.
Title: Characterization of TGF#-associated molecular features and drug responses in
gastrointestinal adenocarcinoma
Version: 6 Date: 15 Apr 2021
Reviewer's report:
1. Regarding the previous question 3: Do you mean that many of the mutations and CNVs in
Fig. 2b lead to loss of function of TGF-b-related genes such as SMAD4? Why does it happen
limited in STAD? The authors should explain it in the main article.
2. Regarding the previous question 4: The authors need to describe how BRAF-V600 inhibitors
affect TGF-b signaling and provide references about it in the main article. It does not mean the
reference should be changed.
3. What is the advantage of using clustering instead of classification by TGF-score in ssGSEA?
Is it because it only requires limited-genes expression data? Is the DNN model useful because
that makes it possible to classify TGF-b subtypes by the only top 10 genes signature? I suggest
that the authors make these points more clear to improve the article.
Please review this paper.
user
Title: Characterization of TGF#-associated molecular features and drug responses in
gastrointestinal adenocarcinoma
Version: 6 Date: 15 Apr 2021
Reviewer's report:
1. Regarding the previous question 3: Do you mean that many of the mutations and CNVs in
Fig. 2b lead to loss of function of TGF-b-related genes such as SMAD4? Why does it happen
limited in STAD? The authors should explain it in the main article.
2. Regarding the previous question 4: The authors need to describe how BRAF-V600 inhibitors
affect TGF-b signaling and provide references about it in the main article. It does not mean the
reference should be changed.
3. What is the advantage of using clustering instead of classification by TGF-score in ssGSEA?
Is it because it only requires limited-genes expression data? Is the DNN model useful because
that makes it possible to classify TGF-b subtypes by the only top 10 genes signature? I suggest
that the authors make these points more clear to improve the article.
assistant