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TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks

Cyrille Lepoivre12, Aurélie Bergon12, Fabrice Lopez123, Narayanan B Perumal4, Catherine Nguyen123, Jean Imbert123 and Denis Puthier15*

Author Affiliations

1 TAGC UMR_S 928, Inserm, Parc Scientifique de Luminy, Marseille, France

2 Université de la Méditerranée, AMU, Parc Scientifique de Luminy, Marseille, France

3 TGML, IBiSA Platform, Parc Scientifique de Luminy, Marseille, France

4 Translational Science, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, USA

5 ESIL, Universités de Provence et de la Méditerranée, Parc Scientifique de Luminy, Marseille, France

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BMC Bioinformatics 2012, 13:19  doi:10.1186/1471-2105-13-19

Published: 31 January 2012

Additional files

Additional file 1:

"Number of predicted motifs versus GC content of PWMs". Each point corresponds to the results obtained using one PWM on mouse genome. The name of a representative transcription factor for each PWM is displayed together with the PWM identifier (informations are separated using a pipe character). The size of the point is correlated with info content of the corresponding matrix).

Format: PDF Size: 21KB Download file

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Open Data

Additional file 2:

"Summary of functional enrichment analysis using ClueGO cytoscape plugin". We estimated the number of predicted regulators for each gene of the human genome by computing the number of non-redundant position-specific motifs associated with each genes. Genes in the top 1% regards to the number of regulators were used as input for the ClueGO plugin.

Format: PDF Size: 10KB Download file

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Open Data

Additional file 3:

"Summary of functional enrichment analysis using ClueGO cytoscape plugin". We estimated the number of predicted regulators for each gene of the mouse genome by computing the number of non- redundant position-specific motifs associated with each genes. Genes in the top 1% regards to the number of regulators were used as input for the ClueGO plugin.

Format: PDF Size: 21KB Download file

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Open Data

Additional file 4:

"TFBS predictions in the mouse genome". A bed file containing TFBS predictions in the mouse genome. 1 - chrom - The name of the chromosome. Fields contain the following informations: chromStart - The starting position of the feature in the chromosome; chromEnd - The ending position of the feature in the chromosome; name - PWM identifier and representative names; score - A score for the PWM hit; strand - Defines the strand - either '+' or '-'; gene id - The gene id of the target gene; geneSymbol- The genesymbol of the target gene.

Format: PDF Size: 19KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5:

"TFBS predictions in the human genome". A bed file containing TFBS predictions in the human genome. 1 - chrom - The name of the chromosome. Fields contain the following informations: chromStart - The starting position of the feature in the chromosome; chromEnd - The ending position of the feature in the chromosome; name - PWM identifier and representative names; score - A score for the PWM hit; strand - Defines the strand - either '+' or '-'; gene id - The gene id of the target gene; geneSymbol- The genesymbol of the target gene.

Format: BED Size: 5.7MB Download file

Open Data

Additional file 6:

"InteractomeBrowser functionalities". Contains a web link to a screencast showing basic use of InteractomeBrowser plugin.

Format: BED Size: 4.7MB Download file

Open Data

Additional file 7:

"Subset of Gene Ontology used for the cell compartment-based layout". Hierarchical structure of the subset of Gene Ontology used in InteractomeBrowser for the cell compartment-based layout. Colors highlight the main compartments.

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Open Data