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Results of Project dynamic_sample
   
 
All the data produced by our analysis are here. There are three files and several directories.

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

File "pic.network" describes the network composing of top genes, which have most dramatic histone modification pattern change in promoter region, and their TF binding target genes if available. Lines with "MG/"(for mark-gene) show the top x genes which have highest value change for the mark. The number following "MG/" is the difference score. Lines with "TG/"(for TF-gene) or "TT/"(for TF-TF) show the regulating of first gene, at the same time encoding a TF, to the second gene (if it is also encoding TF, in second column it would be TT). Sometimes a gene which encodes TF regulates itself.

File "sum.table" describes how many direct targets and indirect targets of the mark there are.

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 histone modification signals in this gene's promoter under two states. It aims to draw a histogram in ".png" file. 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 is available only if the direct target gene encodes TF and it regulates any genes in the uploaded gene list. In column one is the target gene's name. In column two to four are the chromosome, start point and end point of the TFBS in this gene. In column five the sigil denotes which strand this TFBS is in. In column six is the source of the PWM of the TF binding motif.
".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.