Open Access Highly Accessed Research article

The role of Transposable Elements in shaping the combinatorial interaction of Transcription Factors

Alessandro Testori13*, Livia Caizzi12, Santina Cutrupi15, Olivier Friard1, Michele De Bortoli13, Davide Cora'14* and Michele Caselle16*

Author Affiliations

1 Center for Molecular Systems Biology, University of Turin, c/o IRCC - Str. Prov. 142 Km. 3.95, Turin, Candiolo, I-10060, Italy

2 Bioindustry Park Silvano Fumero, Colleretto Giacosa, Italy

3 Department Oncological Sciences, University of Turin, Str. Prov. 142 Km. 3.95, Turin, I-10060, Italy

4 Systems Biology Lab, Institute for Cancer Research and Treatment (IRCC), Str. Prov. 142 Km. 3.95, Turin, Candiolo, I-10060, Italy

5 Department of Life Sciences and Systems Biology, University of Turin, v. Acc. Albertina 13, Turin, 10123, Italy

6 Department of Physics, University of Turin, v. P. Giuria 1, Turin, I-10125, Italy

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BMC Genomics 2012, 13:400  doi:10.1186/1471-2164-13-400

Published: 16 August 2012

Additional files

Additional file 1:

Additional Text and Methods. Content is divided in the following sections: List of Additional Tables, Transposable Elements Annotation, Monte Carlo Simulation, Transcription Factor Binding Sites Identification, Correlators Identification, ER logo, Half-ERE logo.

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Additional file 2:

Additional Tables S1 to S11.

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Additional file 3:

Figure S1. The heat map shows the fraction of enriched transposable elements in the CM dataset which carry particular computationally predicted transcription factor binding sites. Here only a selection of the most important known cofactors of ERα is considered.

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Additional file 4:

Figure S2. The heat map shows the fraction of enriched transposable elements in the E2T datasets which carry particular computationally predicted transcription factor binding sites. Here only a selection of the most important known cofactors of ERα is considered.

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Additional file 5:

Figure S3. The figure shows alignment of MIRs from both CM dataset and E2T dataset. The first line of the figure is MIR core sequence (Smit et al., 1995); the binding site of half-ERE is in red. Following there are all other MIRs. Red is for half-ERE binding site, blue is for AP1 binding site and green is for RORalpha binding site. If the character in the alignment matches the character in the core sequence, it is depicted in bold.

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