| Only-TFs Network |
This table shows the network done with all TFs for which its regulatory coordinates was indicated. Format is as follows: a TFx-TFy interaction per row (where the first putatively regulates the second one), coordinates where the TFx motif was found, strand and position starting from first coordinate and matrix-scan's related score |
| Indirect Interactions |
This file lists indirect interactions (composed by three nodes), as well as direct interactions and no interactions for all TFs. Putative interaction (or binding) information is given as in 'Only-TFs Network'. |
| Complete Network |
This table shows the network done with all the genes for which its regulatory corrdinates was indicated. Format is as follows: a TF-gene interaction per row, coordinates where the TF moif was found, strand and position starting from first coordinate and matrix-scan's related score. |
| Log |
This file specifies each step of the program, posible errors, warnings (e.g. which genes were actually taken into account), and execution time. |
| Newly Found Interactions |
This table lists interactions found by the program but that were not indicated in the input network. Format is as in 'Complete Network'. |
| Networks Overlap |
This table shows the intersection of interactions between the input network and the complete network outputted by the program. Format is as in 'Complete Network'. |
| Not Found Interactions |
This table lists interactions indicated in the input network but that were not corroborated by the program. Format is a gene-gene interaction per row. |
| Used Regulatory Regions FASTA |
Here are the regulatory sequences in FASTA format for all the genomic coordinates indicated in 'Used Regulatory Regions BED' file. |
| Used matrix-scan Results |
Here are the results outputted by matrix-scan used to build the networks. |
| Used PSSMs TRANSFAC |
Here are listed the used Position-Specific Score Matrixes (PSSMs) used to find the indicated TFs' motifs in TRANSFAC format. |
| Used Regulatory Regions BED |
Here is the used BED file with the coordinates of the regulatory regions of each gene. |
