C-CorA: A Cluster-Based Method for Correlation Analysis of RNA-Seq Data

Round 1

Reviewer 1 Report

The Ms entitled “C-CorA: A cluster-based method for correlation analysis of 2 RNA-Seq data” discussed a tool for cluster-based correlation analysis for fruit RNA-Seq data.

Although, there are several methods available for these kind of analysis, but the proposed method will be an additional advantage especially for fruit data analysis.

This Ms can be accepted for publication after further validation with other fruits data.

Since, the method cannot differentiate been the RNA seq data of different plant parts, how and why this tool is only specified for fruits RNA seq data?

They should also demonstrate with some other fruits data, atleast two more fruits data should be analysed to claim the method specific for fruit data analysis, because each fruit has different issues.

Author should demonstrate the validity of this method with some other RNA seq data also. They can find numerous feely available data in the database for this purpose.

Introduction should be focussed around the theme of Ms, Authors have discussed so many unrelated things.

Further, I could see several typographical and grammatical error in the Ms, some of them are listed here, moreover author should carefully revise the complete Ms.

Lines 11-14 should be improved and more clear.

Lines  37-38. here is a need of deep revision of every line.

Lines  41 to 44 should be mentioned clearly.

Lines  51 to 52 is confusing. It should be rewritten.

Lines  52 to 54 is found to be incomplete. It should be elaborated.

In Line  58, what is the meaning of the word ‘hybrid genome’ here? Is it referred to complex or polyploidy or anything else?

Lines  59-61 is not clear. It should be rewrite.

Lines  91-92, should be rewritten.

 Lines  99-100 should be rephased.

Lines  233-234 and 266-267 should be clearly written.

 

Author Response

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Author Response File: Author Response.docx

Reviewer 2 Report

Review of the manuscript “C-CorA: A cluster-based method for correlation analysis of 2 RNA-Seq data” submitted to the Journal of Horticulturae. In this manuscript, the authors presented a tool called C-CorA that is designed to carry out correlation analysis on two RNA-Seq datasets that are already clustered based on their expression profiles. Indeed, this is coherent that correlation application of gene expression data is the foundation for the detection of gene networks as well as hub genes; and clustering the genes priori to this based on their expression profile can give resolution and better outcome to the results. However, I am troubled that the tool provided does not offer significant novel features compared to the already available tools or not presented well for all the features if any implemented.

In addition, I do not find the discussion of the results nor the presentation of the tool much appealing. I believe the authors should make a better effort in presenting the work and its novel features, if any, to target any possible publication.

Author Response

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Author Response File: Author Response.docx

Reviewer 3 Report

The paper by Qian et al. "C-CorA: A cluster-based method for correlation analysis of 2 RNA-Seq data" is devoted to the correlation analysis between the lignification extent in Eriobotrya japonica fruits and the content of transcripts of the genes of these plants in order to determine the genes involved in the lignification process. The study represents a new method of correlation analysis of the genes of woody plants which have a long life cycle and a relatively large and hybrid genome. The authors emphasize that this method can be applied for gene detection in fruit quality study. It seems that the presented method can be used not only for the analysis of fruits, but also more broadly, for the analysis of changes occurring in perennial plants with a long life cycle. 

I can only make a few remarks. The last paragraph in the Introduction section seems a bit unstructured. It seems like that the sentence, lines 76-77 "Some transcription factors have been reported to be involved in the loquat fruit lignification process, including EjMYB1/2 [14], EjMYB8 [15], and EjAP2-1 [16]." should be after the sentence in the line 73 or somewhere else. It breaks the narrative if it is between the sentences “This chilling-induced lignification can be alleviated by an initial low-temperature conditioning (LTC; 5 °C for 6 days 74 followed by transfer to 0 °C) or heat treatment (HT; 40 °C for 4 h followed by transfer to 75 0 °C).” and “In our previous study [17], we compared transcriptome profiles of loquat fruit samples under LTC or HT with those stored at 0°C at five time points from day 1 to day 8 after treatment”. Authors should read carefully the part from the line 71 to the line 86 and revise it.

L. 133. "This approach are highly adaptable" should be corrected.

Captions to tables and figures should be understandable without referring to the text.  For example, "Table 1. The count of correlated genes..." The genes correlated with what? "Figure 6. The RPKM for the candidate genes..." Candidate for what? 

Generally, the authors have carried out a thorough, thoughtful study, which undoubtedly deserves the publication.

Author Response

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Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

The authors have addressed all the concerns. The manuscript can now be accepted. 

Author Response

Thans a lot for your approval