Identification of Enhancers and Promoters in the Genome by Multidimensional Scaling

Round 1

Reviewer 1 Report

The manuscript needs English proofreading.

Author Response

The manuscript needs English proofreading.

The English of my manuscript was proofread by Editage on October 9th.

Reviewer 2 Report

The authors present an approach to search enhancers and promoter regions from Hi-C data. They applied MDS (multidimensional scaling) and found DNA loops from the reconstructed the genome structures. The idea is interesting, but there are several issues to be improved.

1. Previously, some studies tried to use MDS to analyze the Hi-C data. The authors should clarify what is the differences from the previous works.

2. The authors used some metrics as shown at Materials and Methods. For an instance, they defined d_ij new at Eq (1). However, there is no enough explanation and the basis of the formula.

In this time, It is hard to judge whether these metrics make sense.

3. The validation of the experimental results is not enough. The authors' proposed method may identify some of the enhancers and promoter regions. However, it is not clear the method is better, even though the authors already discussed the advantages of their methods comparing to TAD-based approaches. 

Author Response

Please see the attachment.

Round 2

Reviewer 2 Report

The authors addressed the previous concerns by the reviewer.

For publication, I suggest that the authors improve the figures and their legends for the general readers.