|Dataset:||Heat Shock||AIY||Mec regulon|
|Browse Motifs: help|
|Gbrowse Annotation Files for Motif Instances help|
|Cytoscape Session Files help|
|Intermediate Data Files help|
This web page lets you explore the datasets from the paper, and download relevant annotations for use with genome databases. The various options are described here.
Browse Motifs will display the following for each clique in the dataset:
These pages were produced from the sqlite database files using python scripts that are included in the "export" directory of the MCMR package.
In order to view the instances of all motifs on the genome, download the gbrowse annotation files and then click on the "Genome" link at wormbase . Scroll down to "Add your own tracks", in the "Upload a file" section click on "Browse..." and select the file you have downloaded. Now, instances of the motifs should appear in the genome browser. GBrowse is the genome browser provided by the GMOD project, and is used by wormbase and many other genome databases. GBrowse annotation files are described as part of most gbrowse installations, including wormbase here.
Cytoscape session files can be viewed with the freely available cytoscape program. Download the session files from above as well as the cytoscape program from the cytoscape website. Run Cytoscape and then select "File->Open" and select the session file.
The Data Files are intermediate files produced during the creation of the above output. All of the above data files can be produced from the sqlite database files. Indeed, the sqlite database file is perhaps the best starting point if you would like to produce output for a novel format. The primary purpose of making the other files available is to make it possible to reproduce a subset of the analysis, as detailed in the guide to reproducing the results FIXME.