Discovery of Relevant Response in Infected Potato Plants from Time Series of Gene Expression Data
Round 1
Reviewer 1 Report
The authors of the paper describe their approach for the analysis of a time series of gene expression data. The topic has some interest. However, I have the following suggestions:
The contribution should be explained in more detail;
Discussion of related work could be improved;
The paper should be revised in Section 3 and 4 for the discussion of experimental result and conclusion.
Author Response
Response to Reviewer 1 Comments
Point 1: The contribution should be explained in more detail.
Response 1: In Discussion we added: “The contribution of the work is in the definition of a novel measure for characterization of a difference between samples in two classes. When gene expression values have stabilized variance in data pre-processing then stratified data randomization can be used to estimate the statistical properties of this measure for genes that do not differ between target and control samples. Genes whose expression values are statistically significantly differently expressed when compared with control samples and that in some time point have statistically significantly changed expression values in the biological response sequence when compared with the previous time point are selected as specific for this biological response. The approach based on Relative Minimal Distance is very simple and efficient in detecting significant genes with strong stringency. It can be applied to any number of target and control samples but its application is particularly justified when the number of samples is very small.”
Point 2: Discussion of related work could be improved.
Response 2: Second paragraph of Introduction has been significantly extended and two new references have been added.
Point 3: The paper should be revised in Section 3 and 4 for the discussion of experimental result and conclusion.
Response 3: In Section 3 we have deleted Table 6 and we have added a paragraph with the detailed description of the results. In Section 4 we have added two paragraphs, one describes the significance of the work for experimental life sciences research and the other describes how statistical significance of the obtained result can be increased.
Point 4: Are the methods adequately described? Must be improved.
Response 4: In Section 2 we have added a new figure which illustrates changes of real gene expression values in time and how RMD values correspond to differences between real gene expression values for target and control samples. The existing Figure 3 (now Figure 4) has been improved with more details in order to better illustrate statistical properties of randomized gene expression data. A new text describing the figures has been added.
Point 5: Are the conclusions supported by the results? Must be improved.
Response 5: Discussion of the relevance of the results in Section 4 has been significantly improved.
Reviewer 2 Report
In this study, the authors provide a methodology to identify differential expression genes utilizing time-series data. They focus on potato infection data to present their methodology.
I have the following questions/comments:
What does "changes of infected values" refer to in line 18? Particularly, what is an infected value?
Could you elaborate on the compatible potato-PVYNTN interaction?
I found both Figure 1 and 2 very helpful in understanding the methodology. However, the gene expression values and RMDs given in Tables 2-4 could be better presented in a graph format. Also, information in Table 6 could just be given in the text as there are only a few gene functions listed.
Please avoid using vague terms such as "pretty sure" in line 357, instead an estimate of accuracy could be given if possible.
Author Response
Response to Reviewer 2 Comments
Point 1: What does "changes of infected values" refer to in line 18? Particularly, what is an infected value?
Response 1: Corrected: “We aim at identifying differentially expressed genes whose expression values are statistically significantly different between the sets of infected and non-infected potato plants, as well as the statistically significant changes of expression values of genes of PVY infected plants in time.”
Point 2: Could you elaborate on the compatible potato-PVYNTN interaction?
Response 2: Added into Introduction “Compatible interaction is a term, broadly used in plant pathology referring to interaction between pathogen and the plant that leads to successful infection; while incompatible interaction stands for successful plant resistance: i.e., the host’s ability to limit pathogen multiplication”
Point 3: I found both Figure 1 and 2 very helpful in understanding the methodology. However, the gene expression values and RMDs given in Tables 2-4 could be better presented in a graph format. Also, information in Table 6 could just be given in the text as there are only a few gene functions listed.
Response 3: Table 2 is eliminated and its content is presented by a new Figure 3. Tables 3 and 4 (now as Tables 2 and 3) are left without changes but previous Figure 3 (now Figure 4) is modified so that it visually illustrates one example from data in these tables. Table 6 is omitted and its content is presented in text.
Point 4: Please avoid using vague terms such as "pretty sure" in line 357, instead an estimate of accuracy could be given if possible.
Response 4: Corrected: “This means that the relevance of the uncovered genes in terms of their differential expression is statistically justified, but that we cannot be sure that the resulting set of relevant genes is complete.”
Point 5: (x) Moderate English changes required
Response 4: Extensive improvements in many details have been done. Due to their very large number they are not marked by track changes option.
Point 6: Does the introduction provide sufficient background and include all relevant references? Must be improved.
Response 6: Second paragraph of Introduction has been significantly extended and two new references have been added.
Point 7: Are the results clearly presented? Must be improved.
Response 7: One new figure is added, one figure is improved. A new text describing the figures has been added. Discussion of the results is extended.
Round 2
Reviewer 2 Report
The manuscript was improved with the new additions. I would like to thank the authors for their efforts.
