Open Access Methodology article

The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes

Sebastian Vlaic1*, Wolfgang Schmidt-Heck1, Madlen Matz-Soja2, Eugenia Marbach2, Jörg Linde1, Anke Meyer-Baese3, Sebastian Zellmer4, Reinhard Guthke1 and Rolf Gebhardt2

Author Affiliations

1 , Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Beutenbergstr. 11a, D-07745 Jena, Germany

2 Institute for Biochemistry, Faculty of Medicine, University of Leipzig, Johannesallee 30, D-04103 Leipzig, Germany

3 Department of Scientific Computing, Florida State University, Florida 32310-4120, Tallahassee, USA

4 , GermanFederal Institute for Risk Assessment, Max-Dohrn Str. 8-10, D-10589 Berlin, Germany

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BMC Systems Biology 2012, 6:147  doi:10.1186/1752-0509-6-147

Published: 29 November 2012

Additional files

Additional file 1:

Detailed table of differentially expressed genes. Table of the differentially expressed genes containing the corresponding BrainarrayID, EntrezID, GenSymbol, assigned cluster number and the mean expression values at each time point.

Format: XLS Size: 226KB Download file

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Additional file 2:

Enrichment analysis results of the DEGs. Details of the gene enrichment analysis using all differentially expressed genes.

Format: XLS Size: 41KB Download file

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Additional file 3:

Enriched GO-terms and KEGG-pathways of the single clusters. Significant GO biological process (GO-BP) terms and KEGG-pathway (KEGG) terms for each cluster returned by GOstats.

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Additional file 4:

Transcription factor network. Cytoscape session of the transcription factor network shown in Figure 5.

Format: CYS Size: 21KB Download file

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Additional file 5:

In silico knock-down simulation. An image of the network simulation results of the in silico Tgif1 knock-down.

Format: PNG Size: 324KB Download file

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Additional file 6:

Performance analysis of ExTILAR. A performance analysis of ExTILAR using in silico data for a systematic inference. The results are compared to the results of the NetGenerator algorithm.

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