Open Access Highly Accessed Research article

Genome-wide inference of regulatory networks in Streptomyces coelicolor

Marlene Castro-Melchor1, Salim Charaniya14, George Karypis2, Eriko Takano3 and Wei-Shou Hu1*

  • * Corresponding author: Wei-Shou Hu wshu@umn.edu

  • † Equal contributors

Author Affiliations

1 Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Avenue SE, Minneapolis, MN 55455, USA

2 Department of Computer Science and Engineering, University of Minnesota, 200 Union Street SE, Minneapolis, MN 55455, USA

3 Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands

4 Genentech, Inc, 1 Antibody Way, Oceanside, CA 92056, USA

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BMC Genomics 2010, 11:578  doi:10.1186/1471-2164-11-578

Published: 18 October 2010

Additional files

Additional file 1:

Conserved pairs. Column 1 and 2 contain the pair of genes, column 3 the probability, and column 4 the number of genomes in which the pair is conserved.

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Additional file 2:

Training set. Column 1 and 2 contain the pair of genes, and column 3 its status as KOP or NOP.

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Additional file 3:

Operon predictions. Column 1 contains genes, and column 2 contains the operon into which the gene was predicted.

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Additional file 4:

Network predictions. Rows represent network elements, columns indicate network modules and the cistron containing the regulatory gene. Numbers are MI values, higher MI values indicate higher correlation.

Format: CSV Size: 3.7MB Download file

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Additional file 5:

Summary of the consensus sequences found in the networks. For each network the values E-valuethreshold and E-value are given. The number of motifs detected and if applicable its consensus sequence are given, together with the total number of elements in the module and the number of elements in which the consensus sequence was detected.

Format: CSV Size: 57KB Download file

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Additional file 6:

Enriched networks. Worksheet 1 contains the list of network modules enriched according to the protein classification scheme, and worksheet 2 those enriched according to GO terms. For each of the enriched network modules the p-value, q-value and the enriched class or term is given. All network modules are significant at an FDR = 0.01.

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Additional file 7:

Details of the 20 network modules enriched in both a protein class and a GO term. The number of cistrons in the network module and the consensus sequence detected in all its members is given.

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Additional file 8:

Additional network modules enriched and with consensus sequence. Network modules 20, 45, 636, and 691 enriched in a protein class and a GO term and containing a consensus sequence in all of its members (see Table 2 and additional file 7).

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