Open Access Research article

Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia

Ivan Ishchukov1, Yan Wu1, Sandra Van Puyvelde1, Jos Vanderleyden1 and Kathleen Marchal123*

Author Affiliations

1 Center of Microbial and Plant Genetics, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium

2 Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium

3 Department of Information Technology, Ghent University, IMinds, VIB, 9052 Gent, Belgium

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BMC Microbiology 2014, 14:14  doi:10.1186/1471-2180-14-14

Published: 27 January 2014

Additional files

Additional file 1: Table S1:

Characteristics of module network as reconstructed by CLR and LeMoNe.

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Additional file 2: Table S2:

Overview of the sRNAs in the different modules.

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Additional file 3: Table S3:

Performance of inferring sRNA-target interactions.

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Additional file 4:

Module overview.

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Additional file 5: Table S4:

Description of the expression compendium.

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Additional file 6: Table S5:

Probe information.

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Additional file 7:

Performance tests to optimize sequence-based sRNA-target predictions.

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Additional file 8: Table S6:

Predictions of sRNA targets based on intaRNA and TargetRNA.

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Additional file 9: Table S7:

List of regulators.

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Additional file 10: Table S8:

Description of our benchmark of known sRNA-target interactions.

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