Open Access Open Badges Methodology article

Localizing potentially active post-transcriptional regulations in the Ewing's sarcoma gene regulatory network

Tatiana Baumuratova123*, Didier Surdez45, Bernard Delyon23, Gautier Stoll678, Olivier Delattre45, Ovidiu Radulescu1011239 and Anne Siegel111213

Author Affiliations

1 Systems Biology Group, Life Science Research Unit, University of Luxembourg,162A Avenue de la Faiencerie, Luxembourg, L-1511, Luxembourg

2 Work done at: IRMAR, Université de Rennes 1, Rennes, France

3 UMR 6625, CNRS, Rennes, France

4 Genetics and Biology of Cancers, Institut Curie, Paris, France

5 Unité 830, INSERM, Paris, France

6 Service bioinformatique, Institut Curie, Paris, France

7 Unité 900, INSERM, Paris, France

8 Service bioinformatique, Mines ParisTech, Fontainebleau, France

9 DIMNP, Université de Montpellier 2, Montpellier, France

10 UMR 5235, CNRS, Montpellier, France

11 Symbiose project team, INRIA, Rennes, France

12 UMR 6074, CNRS, Rennes, France

13 IRISA, Université de Rennes 1, Rennes, France

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BMC Systems Biology 2010, 4:146  doi:10.1186/1752-0509-4-146

Published: 2 November 2010

Additional files

Additional file 1:

Interaction graph adapted from original network. The non-modified interaction graph (no differentiation between mRNAs and proteins done) is shown in the file 'Additional file 1.csv', which is structured to be readable by the BioQuali tool.

Format: CSV Size: 10KB Download file

Open Data

Additional file 2:

Modified interaction graph. 'Additional file 2.cvs' contains the network which includes all modifications as described in the text of the paper. It is also in a BioQuali-readable format of interaction network representation.

Format: CSV Size: 12KB Download file

Open Data

Additional file 3:

Results of statistical analysis of microarray data [21]. 'Additional file 3.xls' comprises calculated slopes, variations and corresponding p-values for microarray data of gene responses on both inhibition and recovery of EWS-FLI1. All the transcript variants of genes present in our network model were grouped and the statistical tests were applied to such 'gene' data rather than 'transcript variant' data, to give a comprehensive picture of gene behaviors.

Format: XLS Size: 56KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 4:

Set of experimental observations. 'Additional file 4.csv' file presents the observation dataset resulting from the statistical analysis of microarray data shown in Additional file 3.

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Open Data

Additional file 5:

Results of the constraint-based analysis. 'Additional file 5.xls' contains the results of constraint-based modeling of the extended EWS-FLI1 regulatory network with the integrated experimental observations set. The first column shows the discovered inconsistencies (while analyzing the original interaction network). The following columns display the consistency of the modified network (mRNA nodes included) with the dataset and predictions obtained after the analysis.

Format: XLS Size: 35KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data