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Since all the critiques were adequately addressed and the manuscript was revised accordingly, the amended version is acceptable now.
[# PeerJ Staff Note - this decision was reviewed and approved by Paula Soares, a PeerJ Section Editor covering this Section #]
Please address issues pointed by the reviewers and revise the manuscript accordingly.
[# 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/ #]
Meng et al.performed WGCNA to identify hub genes in the tumourigenesis of CRC. By combining data from TCGA and GEO, they identified ten hub genes (MT1X, MT1G, MT2A, CXCL8, IL1B, CXCL5, CXCL11, IL10RA, GZMB, KIT) and closely related to the progression of CRC. They performed a lot of computational analysis to validate their findings.
The experimental design is reasonable
1. In the result "GO functional and KEGG pathway analyses of mRNAs", could the author show some specific biological processes or pathways that are involved in the progression of CRC?
2. Please clarify your reasoning for selecting GSE28000 and GSE42284 for analysis from the GEO database.
3. This article identifies 10 related genes (MT1X, MT1G, MT2A, CXCL8, IL1B, CXCL5, CXCL11, IL10RA, GZMB, KIT) closely related to the progression of CRC were identified. Why IL10RA and KIT related to overall survival time?
1. The author's full text is too simple, and it is suggested to elaborate in detail, for example: introduction part (Please describe your rationale for selecting your candidate genes in the Introduction), result expression part.
2. I would suggest the authors to increase the figure resolution. It's hard to see clearly the texts in most figures.
3. In the result "GO functional and KEGG pathway analyses of mRNAs", could the author show some specific biological processes or pathways that are involved in the progression of CRC?
4. Please clarify your reasoning for selecting GSE28000 and GSE42284 for analysis from the GEO database.
5. There are some format errors in this article, which need to be modified.
6. This article identifies 10 related genes (MT1X, MT1G, MT2A, CXCL8, IL1B, CXCL5, CXCL11, IL10RA, GZMB, KIT) closely related to the progression of CRC were identified. Why IL10RA and KIT related to overall survival time?
The authors constructed a prognostic model based on the candidate ten genes by using the data set GSE28000 and GSE42284. WGCNA，co-expression network and the PPI network were used to screen hub genes. Survival analysis suggested that IL10RA and KIT were significantly associated with the prognosis of patients.Overall, the authors performed a lot of validation work for CRC.I still have some concerns.
The experimental design is reasonable
1.Why did the authors select GSE28000 and GSE42284 for further analysis?
2.The pre-processing procedures of the TCGA and GEO RNA-Seq datasets should be explained in detail.
3.The title of this article is“Identification of 10 Hub genes related to the
progression and prognosis of colorectal cancer by co-expression analysis”.Why survival analysis suggested that only IL10RA and KIT were significantly associated with the prognosis of patients, how about survival analysis of other eight genes?
4.I would suggest the authors to increase the figure resolution. It's hard to see clearly the texts in most figures.
1. Authors have done a sloppy job in writing the entire manuscript. English check/edits are required to make the article easy to understand.
2.The authors should re-check of language mistakes in the revised version.
I think the article is well written, the logic is clear, the research content is reliable, and the science is good, which basically meets the publication requirements of the magazine.
It's a very good study. And the aim of this study is clear. Methods described sufficient detail & information to replicate. Some researchers may interest in it.
This manuscript is well written and novely, I think that it has the potential for acceptance of peer j.
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