All reviews of published articles are made public. This includes manuscript files, peer review comments, author rebuttals and revised materials. Note: This was optional for articles submitted before 13 February 2023.
Peer reviewers are encouraged (but not required) to provide their names to the authors when submitting their peer review. If they agree to provide their name, then their personal profile page will reflect a public acknowledgment that they performed a review (even if the article is rejected). If the article is accepted, then reviewers who provided their name will be associated with the article itself.
The manuscript is being accepted for publication since the authors have addressed all comments from reviewers.
[# PeerJ Staff Note - this decision was reviewed and approved by Keith Crandall, a PeerJ Section Editor covering this Section #]
Grammar need to corrected in line 35. "up-regulation" should be "up-regulated".
No comment
No comment
Very detailed and covered all the queries.
All the comments were properly addressed.
N/A
N/A
Thank you for properly addressing the comments!
The revision looks good.
The revision looks good.
The revision looks good.
The revision looks good.
The manuscript is suitable to be published.
The manuscript is suitable to be published.
The manuscript is suitable to be published.
The manuscript is suitable to be published.
Please address all reviewer comments and feedback.
[# PeerJ Staff Note: Please ensure that all review comments are addressed in a rebuttal letter and any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate. It is a common mistake to address reviewer questions in the rebuttal letter but not in the revised manuscript. If a reviewer raised a question then your readers will probably have the same question so you should ensure that the manuscript can stand alone without the rebuttal letter. Directions on how to prepare a rebuttal letter can be found at: https://peerj.com/benefits/academic-rebuttal-letters/ #]
The study was carried out with detailed bioinformatics approach. Reasonable references were used to cover all the background about the research. The figures and tables are clear to understand the goal of the study. Also the results are focused.
Few points would be important to add,
1. Are the normal tissues collected from the adjacent part from of HCC patients?
2. It would be important to know if HCC patients had any other health conditions.
Experimental designs are hypothesis directed and answered most of the necessary questions. Also, the experimental approaches are reasonable and precise. The methods are explained in full details.
The findings are interesting and this study has provided sufficient data to strengthen their hypothesis.
Very detailed approach.
The writing is well organized and professional
The details of the analysis is well described
The methods are well described and that support their findings of the targets at the RNA level. However, a few more additional experiments will enhance the quality of the paper.
This article aims to identify markers for overall survival in HCC. Overall the methods are well detailed and the analysis well presented. The authors have identified some of the shortcomings such as validation of protein. Some of my comments are as follows
1. Line 178 - 5 genes were altered in 93 (25%) of 372 samples. This appears to be a small percentage and sample size to be a marker without any protein verification. Any verification at the protein level is important and will increase the impact of the paper,
2. Discussion lines 199 to 220 – For most targets, the authors have mentioned how they might have an important role but does not describe the role in details. Kindly elaborate the discussion further.
This is a well-written manuscript that identified a prognostic model with 5 genes by transcriptomic analysis on hepatocellular carcinoma databases. This 5 gene-based risk model was further validated by TCGA-LIUC and GSE14550 databases.
Some comments:
1. In the introduction, the authors need to introduce the current gap of the prognosis model for liver cancers and how this study can fill the gap.
2. Figure 1, I would suggest the authors to include a supplementary table listing the 15% upregulated genes in the tumor tissues. This would help increase the impact by allowing further exploration of the signatures by readers.
3. Are these 5 genes relevant to the clinical-pathological characteristics of the disease such as TNM stage, pathological type. etc?
The results have some promise but given the contradictory nature can you back it up with some experimentation to validate the finding?
No.
There are several grammatical mistakes at different places in the manuscript. For example in the methods part of the highlight section in the beginning there is a sentence that ends abruptly (" Then, gene set enrichment analysis (GSEA) was used to identify. "). There are several such mistakes and the authors should carefully review and correct these grammatical errors.
The literature review provided by the authors is very brief and almost irrelevant. Readers and reviewers would definitely gain from knowing other research efforts to identify prognostic gene expression based biomarkers in HCC or even other types of cancers.
The experiment design and the analysis performed by the authors was thorough. However, it would be beneficial if they compared their work and results with other efforts to identify gene-expression based biomarkers.
The authors showed convincingly that their 5-gene signature was sufficiently predictive of OS and PFS.
The analysis was straightforward and easy to follow. The authors clearly show the prognostic power of the 5-gene expression based signature in HCC. Some literature review and relevant to the point motivation for the study will help readers appreciate the work.
Manuscript details
Journal: Peerj
Manuscript ID: Peerj - 55265
Type of manuscript: Article
Title: Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma
In this manuscript entitled “Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma”. There is some useful information, however, the further modification is required, and I have provided several advices shown below.
1. This article uses a lot of data analysis, but the main reason for selecting these dataset is not very clear. I hope the author can discuss it in detail.
2. The data has been analyzed in many aspects. Due to the wide range of genetic influences, it is recommended to use genetically modified mice for further research.
3. The authors only discussed the mortality of genes. I suggested that related drug development strategies should also be discussed together
To sum up, the manuscript should be minor revision.
Reasonable experiment design
Manuscript details
Journal: Peerj
Manuscript ID: Peerj - 55265
Type of manuscript: Article
Title: Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma
In this manuscript entitled “Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma”. There is some useful information, however, the further modification is required, and I have provided several advices shown below.
1. This article uses a lot of data analysis, but the main reason for selecting these dataset is not very clear. I hope the author can discuss it in detail.
2. The data has been analyzed in many aspects. Due to the wide range of genetic influences, it is recommended to use genetically modified mice for further research.
3. The authors only discussed the mortality of genes. I suggested that related drug development strategies should also be discussed together
To sum up, the manuscript should be minor revision.
Manuscript details
Journal: Peerj
Manuscript ID: Peerj - 55265
Type of manuscript: Article
Title: Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma
In this manuscript entitled “Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma”. There is some useful information, however, the further modification is required, and I have provided several advices shown below.
1. This article uses a lot of data analysis, but the main reason for selecting these dataset is not very clear. I hope the author can discuss it in detail.
2. The data has been analyzed in many aspects. Due to the wide range of genetic influences, it is recommended to use genetically modified mice for further research.
3. The authors only discussed the mortality of genes. I suggested that related drug development strategies should also be discussed together
To sum up, the manuscript should be minor revision.
All text and materials provided via this peer-review history page are made available under a Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.