EpiRegNet aims to build a transcriptional regulatory network composing of histone modification and transcription factor binding in promoters and interactions between factors in these two fields.

All the data produced by our analysis are here. There are four files and several directories.

File "readme.txt" explains the content of each file.

File "output.cor.file" describes the network composing of top ten functional histone modification marks (after sorted in ascending order by p values) and special marks chosen by user followed by their p values.
Lines with "MG/" show the top x genes (x is a parameter, and default value is five) which have highest enrichment scores for each mark. The number following "MG/" is the enrichment score.
Lines with "MM/" show the correlation coefficients between marks. The number following "MM/" is the coefficient. Besides, only if the correlation test produces a p value less than alpha, its coefficient would be displayed.

File "output.mat.cor.file" describes the matrix(heatmap in project results) composing of all histone modification marks.
For each pair of marks, their correlation test p value is in column three and correlation coefficient is in column four.

File "output.mt.cor.file.sorted" describes correlation between each histone modification mark and all functional transcription factors.
In column one is the histone modification mark. In column two is the transcription factor(TF). In column three is the p value of chi-square test or fisher's exact test on the TF(here only if p value is less than alpha it would be shown). In column four is the p value of correlation test. In column five is the coefficient of correlation test, and if the p value is greater than alpha, we assign -2 to the coefficient.

All the directories are named by gene names which compose "network" in result. In each directory, the sub directory is named by accession number of this gene. In the sub directory name, accession number is followed by chromosome, start point, end point and strand(p for positive and n for negative) of this gene, connected by ".". Since one gene name may have several accession numbers, there might be more than one sub directory under one gene name.
In each sub directory, there are three files. Each filename contains information of chromosome, start point and end point of the promoter region.

"hm." file describes five strongest histone modification signals in this gene's promoter. It aims to draw a histogram in ".png" file. In column one is the mark's name. In column two is the chromosome. In column three are the coordinates of breakpoints in the histogram. In column four are the heights(scores) of cells in the histogram.
"tf." file describes all detectable transcription factor binding sites(TFBSs) in this promoter. In column one is the name of TF. In column two is the chromosome of gene. In column three and column four are coordinates of start and end points of TFBS. In column five is the p value of chi-square test or Fisher's exact test on this TF. If the TF type is "motif", column six and seven are strand and source of PWM of the TFBS.
".png" file is the picture drawn based on the information in the above two files. It is the picture in the pop-up window in the web server.