Maximal Clique Motif Reduction : Explore Datasets

Dataset:	Heat Shock	AIY	Mec regulon
Browse Motifs: help
Gbrowse Annotation Files for Motif Instances help	HSP Core Motifs WS160 WS176 HSP Raw Motifs WS160 WS176	AIY Core Motifs WS160 WS176 AIY Raw Motifs WS160 WS176 Wenick and Hobert WS160 WS176	MEC Core Motifs WS160 WS176 MEC Raw Motifs WS160 WS176
Cytoscape Session Files help
Intermediate Data Files help	seqtar and region gff run protocol runtar emf file HSP Sqlite Database	seqtar and region gff run protocol runtar emf file AIY Sqlite Database	seqtar and region gff run protocol runtar emf file MEC Sqlite Database

Instructions

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

Browse Motifs will display the following for each clique in the dataset:

1. Summary of "core" reduced motif of clique, including logo and pie chart inidicating the fraction of input genes covered
2. For each motif in the clique
1. Aligned text string showing orientation and placement of motif relative to others in clique
2. Sequence logo of motif instances as reported by motif finder
3. the number of matches and number of regions for motif
4. The idetity of the motif finder that identified the motif, as well as the order of the motif in that finder's output indexed to 1, as well as the run number and the internal ID of the motif, for purposes of cross referencing with the cytoscape files
5. The name of the gene list the motif finder was run on, as well as a pie chart indicating coverage.

These pages were produced from the sqlite database files using python scripts that are included in the "export" directory of the MCMR package.

GBrowse Annotations

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

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.

Data Files

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.