Bioinformatics and Experimental Analyses Reveal NFIC as an Upstream Transcriptional Regulator for Ischemic Cardiomyopathy

Round 1

Reviewer 1 Report

major comments:

1. line 98: the cutoffs used for DEGs are kind of too high, I would suggest to decrease the fold change cutoff to get more deregulated genes.

2. line 103 and 168: for functional enrichment study the authors only used the down-regulated genes, which can lead to a biased result. 
    because the full list of GEGs is not really long (see comment 1) , I dont see the reason for only choosing downregulated genes.

3. line 167-168: the description of enrichment study is not clear. did the authors use all down-regulated genes (118) from full DEGs or a shorter list from the top50DEGs? 
4. line 194: for the TF binding motif screening step, the text "Previously-obtained down-regulated genes" was not clear.

5. line 198-213: the reason to use IBNS-DEGs to filter the SEA result of Motifs is not convicing. Why not list the top motifs identified after SEA? 

6. line 228 and 239 and Table 4: are the "the predicted 33 genes" mentioned in line 228 is the same as "33 overlapped down-regulated genes were predicted with NFIC-binding motif." in line 239?
    are they all derived from motif prediction, or it means 33 of the results were found down regulated in RNA-seq datasets? 

7. Figure 4: functional enrichment analysis of 33 genes is unnessary and it can not give a siginificant pathway/function hits due to the small number of input genes.

8. Figure 5:  the genes validated with qPCR(fig5F) are not derived from the microarray cross validation(fig5B). please give the reason that why those genes were selected. 

 

minor comments:

1. fig2D: dendrogram tree of samples is missing for the heatmap
2. fig3E-H: what does the rich facor mean in WHEA result? why not plot the FDR or Bonferroni P-values?
3. fig5: bar plot resolution is too low. please indicate the n number for qPCR assays.

Author Response

Thanks for you constructive comments and appreciation！Please see the attachment

Author Response File: Author Response.docx

Reviewer 2 Report

 

The authors try to identify novel transcriptional regulators in ischemic cardiomyopathy in order to use them as an effective method to establish new diagnostic and therapeutic strategies. The article is well-written and comprehensive, with clear and interesting results, that can make significant contributions to clinical practice. The statistical analysis is well done, with clear and legible figures and tables. I consider that the authors should better discuss the novelty of the study and also the potential clinical implications of their results.

Author Response

Thanks for your comment and appreciation

Round 2

Reviewer 1 Report

Questions were properly answered in cover letter of revision, and the manuscript has been largely improved. The authors have added the results for up-regulated genes, which makes the manuscript more comprehensive and reliable.

I would suggest that the authors could also discuss a bit about the reason(s) of focusing on down-regulated genes for this work in the discussion part. 

 

Author Response

I would suggest that the authors could also discuss a bit about the reason(s) of focusing on down-regulated genes for this work in the discussion part. 

RE:Thanks for your appreciation and constructive comments! According to your suggestion, we have added “Transcription activators are cellular regulators that can up-regulate the transcription level of genes by binding to specific short sequences of DNA in the promoters or enhancers of target genes. Many studies have reported that down-regulated transcription activators play important roles in various diseases. Reduced expression of transcription factor FOXP1 and its downstream gene p21^Waf1/Cip1 was found to be a contributing factor in Huntington's disease[39]. The expression of transcription activator FOXO4 is decreased significantly in most gastric cancer tissues and in various human gastric cancer cell lines, suggesting it may serve as a potential therapeutic target for gastric cancer[40]. By the inspiration of these studies, we hope to find the key down-regulated transcription activators and their downstream targets of ICM. Hence, we are more interested in the down-regulated genes and transcription activators” in the fourth paragraph of the discussion part in the revised manuscript.