Author's response to reviews Title: Identifying Significant Genetic Regulatory Networks in the Prostate Cancer from Microarray Data Based on Transcription Factor Analysis and Conditional Independency Authors:

We appreciate the comments from the associate editor and all reviewers in this paper. We have made necessary experiments and modifications to cope with all the comments. The basic notations for different fonts are: Bold face fonts are from reviewers' original comments. Italic face fonts are the modified/added texts in the paper. Plain fonts are our answers to reviewers' comments. Q1: There is a mistake in interpretation of missing value estimation (Section3.1).The formula in step 1 of KNN algorithm should not include the missing value in A while all N samples are calculated. Second, it should be pointed out that only genes without any missing values can be used to impute missing value in gene A, otherwise it's impossible to calculate Euclidean distance by that formula. A1: Thanks for your comments for the mistake in interpretation of missing value estimation. In the step 1 of KNN algorithm, while we impute only one missing values of gene A in microarray data, we should not calculate Euclidean distance with this missing value and modify the formula in Equation(1) that is not included the missing value in A. We have modified. A2: In formula of Euclidean distance, we pointed out that only genes in the experiments without missing values can be used to impute in Equation(1). If genes with missing values in the experiment, we ignore this experiment for calculating Euclidean distance formula. Because we ignore the genes with more than 20% of missing values, there are not many missing data in the microarray data. On P.7 from line 14-22 The steps of KNN algorithm are listed as follows: 1) We consider gene A with the missing value in experiment t and calculate the Euclidean distance between Gene A and other genes without missing values in other t-1 experiment. Suppose (p 1 , p 2 , p t-1 , p t+1 , …, p N) and (q 1 , q 2 , q t-1 , q t+1 ,…, q N) are the expression values of the gene A and other genes in other N-1 experiments. The Euclidean distance between the two gene expressions is as follows: () () () () () () n i i i t t t t q p q p q p q p q p q p 1 2 2 N N 2 1 1 2 1 1 2 2 2 2 1 1 ... If genes with …