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Computational discovery of regulatory elements in a continuous expression space

Mathieu Lajoie*, Olivier Gascuel, Vincent Lefort and Laurent Bréhélin

Author Affiliations

Méthodes et algorithmes pour la Bioinformatique, LIRMM, Univ. Montpellier 2, CNRS; 161 rue Ada, 34095 MONTPELLIER, France

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Genome Biology 2012, 13:R109  doi:10.1186/gb-2012-13-11-r109

Published: 27 November 2012

Additional files

Additional file 1:

Assessment for S. cerevisiae using the JASPAR and the Gordân et al. databases. Results obtained when using the JASPAR and the Gordân et al. databases (instead of ScerTF). This corresponds to the experiments shown in Figures 8 to 10 in the main manuscript.

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Open Data

Additional file 2:

Results of RED2 with mutual information criterion on the S. cerevisiae upstream regions with the Gasch et al. stress compendium. The set of motifs inferred by RED2 on the Gasch et al. complete compendium. Provided for each motif are the logo of the motif, the number of genes that have the motif in their promoter region, the expression profiles (heatmap) associated with the motif, a histogram of the motif occurrence positions, the existence/absence of any strand bias, and the name of the ScerTF motif that best matches the inferred motif (if any at 15% FDR).

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Open Data

Additional file 3:

Results of RED2 (hypergeometric) on S. cerevisiae upstream regions with the Gasch et al. stress compendium. The set of motifs inferred by RED2 on the Gasch et al. complete compendium. See the description of Additional file 2 for table column definitions.

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Open Data

Additional file 4:

Results of RED2 (mutual information) on S. cerevisiae upstream regions with the Spellman et al. cell-cycle dataset. The set of motifs inferred by RED2 on the Spellman et al. dataset. See the description of Additional file 2 for table column definitions.

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Open Data

Additional file 5:

Results of RED2 (hypergeometric) on S. cerevisiae upstream regions with the Spellman et al. cell-cycle dataset. The set of motifs inferred by RED2 on the Spellman et al. dataset. See the description of Additional file 2 for table column definitions.

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Open Data

Additional file 6:

Results of FIRE on S. cerevisiae upstream regions with the Spellman et al. cell-cycle dataset. The set of motifs inferred by FIRE on the Spellman et al. dataset. See the description of Additional file 2 for table column definitions.

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Open Data

Additional file 7:

Results of MatrixREDUCE on S. cerevisiae upstream regions with the Spellman et al. cell-cycle dataset. The set of motifs inferred by MatrixREDUCE on the Spellman et al. dataset. See the description of Additional file 2 for table column definitions.

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Open Data

Additional file 8:

ScerTF motifs recovered by RED2, FIRE and MatrixREDUCE on the 24 S. cerevisiae datasets. For each method, this table provides the number of datasets in which each motif was recovered (at 15% FDR). For example, REDUCE correctly predicts AFT1 (first line) in one dataset. The last two lines give the total number of correct predictions (Total) and the number of distinct motifs recovered (Coverage). For example, for the 24 datasets, RED2 makes 177 correct predictions, which cover 43 distinct motifs in ScerTF.

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Open Data

Additional file 9:

Results of RED2 (mutual information) on P. falciparum upstream regions with the Bozdech et al. dataset (erythrocytic cycle). The set of motifs inferred by RED2 on the upstream regions of P. falciparum genes using the Bozdech et al. dataset [11]. See the description of Additional file 2 for a description of the different columns.

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Open Data

Additional file 10:

Results of RED2 (mutual information) on P. falciparum downstream regions with the Shock et al. dataset (mRNA decay). The set of motifs inferred by RED2 on the downstream regions of P. falciparum genes using the Shock et al. dataset [36]. See the description of Additional file 2 for table column definitions.

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Open Data

Additional file 11:

Results of FIRE on P. falciparum upstream regions with the Bozdech et al. dataset (erythrocytic cycle). The set of motifs inferred by FIRE on the upstream regions of P. falciparum genes using the Bozdech et al. dataset [11]. See the description of Additional file 2 for table column definitions.

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Open Data

Additional file 12:

Results of MatrixREDUCE on P. falciparum upstream regions with the Bozdech et al. dataset (erythrocytic cycle). The set of motifs inferred by MatrixREDUCE on the upstream regions of P. falciparum genes using the Bozdech et al. dataset [11]. See the description of Additional file 2 for table column definitions.

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Open Data

Additional file 13:

The 22 datasets from the Gasch et al. compendium. This text file describes the partition of the Gasch et al. [21] stress compendium into 22 test datasets.

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Open Data