Research article
Comparative analysis of module-based versus direct methods for reverse-engineering transcriptional regulatory networks
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* Corresponding author: Tom Michoel tom.michoel@psb.vib-ugent.be
1 Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium
2 Department of Molecular Genetics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
3 CMPG, Department Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
BMC Systems Biology 2009, 3:49 doi:10.1186/1752-0509-3-49
Published: 7 May 2009Additional 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.
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Additional file 9:
E. coli modules in the LeMoNe 30% precision network. Gene content of E. coli LeMoNe modules in the 30% precision network.
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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.
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Additional file 12:
S. cerevisiae list of candidate regulators. S. cerevisiae list of candidate regulators, used as input for LeMoNe and CLR.
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Additional file 13:
S. cerevisiae reference network. S. cerevisiae reference network of known transcriptional interactions, obtained from reference [12].
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Additional file 14:
S. cerevisiae modules in the LeMoNe 1070 network. Gene content of S. cerevisiae LeMoNe modules in the 1070 network.
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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.
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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