Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

doi:10.1186/1752-0509-3-49

BMC Systems Biology

Volume 3

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Research article

Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks

Tom Michoel¹^,2 , Riet De Smet³ , Anagha Joshi¹^,2 , Yves Van de Peer¹^,2 and Kathleen Marchal³

¹Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium

²Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium

³CMPG, Department Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium

author email corresponding author email

BMC Systems Biology 2009, 3:49doi:10.1186/1752-0509-3-49


Published:	7 May 2009

Additional files

Additional file 1:

LeMoNe network for E. coli at 30% precision cutoff. Supplementary Figure S1.

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Additional file 2:

CLR network for E. coli at 30% precision cutoff. Supplementary Figure S2.

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Additional file 3:

LeMoNe network for S. cerevisiae at first 1070 predictions. Supplementary Figure S3.

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Additional file 4:

CLR network for S. cerevisiae at first 1070 predictions. Supplementary Figure S4.

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Additional file 5:

New interactions predicted in the 30% precision LeMoNe network validated by literature search. Supplementary Table S1.

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Additional file 6:

Expression levels of chemotaxis and flagellar genes in E. coli. Supplementary Figure S5.

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Additional file 7:

E. coli list of candidate regulators. E. coli list of candidate regulators, used as input for LeMoNe and CLR.

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Additional file 8:

E. coli reference network. E. coli reference network of known transcriptional interactions, compiled from RegulonDB and EcoCyc.

Format: TXT Size: 30KB Download file

Additional file 9:

E. coli modules in the LeMoNe 30% precision network. Gene content of E. coli LeMoNe modules in the 30% precision network.

Format: TXT Size: 6KB Download file

Additional file 10:

E. coli regulator to module assignments in the LeMoNe 30% precision network. List of E. coli regulator to module assignments and their score in the LeMoNe 30% precision network.

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Additional file 11:

E. coli CLR 30% precision network. List of E. coli interactions and their score in the CLR 30% precision network.

Format: TXT Size: 27KB Download file

Additional file 12:

S. cerevisiae list of candidate regulators. S. cerevisiae list of candidate regulators, used as input for LeMoNe and CLR.

Format: TXT Size: 2KB Download file

Additional file 13:

S. cerevisiae reference network. S. cerevisiae reference network of known transcriptional interactions, obtained from reference [12].

Format: TXT Size: 52KB Download file

Additional file 14:

S. cerevisiae modules in the LeMoNe 1070 network. Gene content of S. cerevisiae LeMoNe modules in the 1070 network.

Format: TXT Size: 7KB Download file

Additional file 15:

S. cerevisiae regulator to module assignments in the LeMoNe 1070 network. List of S. cerevisiae regulator to module assignments and their score in the LeMoNe 1070 network.

Format: TXT Size: 1KB Download file

Additional file 16:

S. cerevisiae CLR 1070 network. List of S. cerevisiae interactions and their score in the CLR 1070 network.

Format: TXT Size: 21KB Download file