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ReMoDiscovery specifications

Information


Unique identifier OMICS_34292
Name ReMoDiscovery
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for ReMoDiscovery

ReMoDiscovery citations

 (5)
library_books

Passing Messages between Biological Networks to Refine Predicted Interactions

2013
PLoS One
PMCID: 3669401
PMID: 23741402
DOI: 10.1371/journal.pone.0064832

[…] 0.63–0.65 compared to 0.48–0.55 for SEREND, 0.48–0.5 for ReMoDiscovery, 0.53–0.55 for CLR and 0.5 for C3Net. Within the edges that are not supported by motif data PANDA performs slightly better than ReMoDiscovery, CLR and C3Net, with an AUC of around 0.53–0.55 compared to 0.5 for ReMoDiscovery, 0.46–0.53 for CLR and 0.5 for C3Net. Interestingly, SEREND does fairly well on non-motif edges, with an […]

library_books

Inference of hierarchical regulatory network of estrogen dependent breast cancer through ChIP based data

2010
BMC Syst Biol
PMCID: 3012048
PMID: 21167036
DOI: 10.1186/1752-0509-4-170

[…] so found that there are ~40% common TFs regulated by ERα among three different ChIP-based technologies.We also compared the regulatory network in MCF7 constructed by our approach with another method--ReMoDiscovery []. We used 0.9 (for Motif threshold), and 0.5 (for expression correlation threshold) as the input threshold. Total 26 (of 42) nodes were overlapped between our method (Additional file , […]

library_books

Transcriptional programs: Modelling higher order structure in transcriptional control

2009
BMC Bioinformatics
PMCID: 2725141
PMID: 19607663
DOI: 10.1186/1471-2105-10-218

[…] ta are commonly used. Heuristics or probabilistic models are used to search for consistent structure amongst these data sources. Almost all this work has been carried out in Saccharomyces cerevisiae. ReMoDiscovery [] builds on the Apriori framework in a two-step procedure which examines expression profiles and ChIP-chip data. MOFA [] combines binding data with time-series microarray data to build […]

library_books

Identifying gene regulatory modules of heat shock response in yeast

2008
BMC Genomics
PMCID: 2575218
PMID: 18811975
DOI: 10.1186/1471-2164-9-439

[…] ll cycle. More data sources were used in more recent studies. Kato et al. [] identified GRMs of yeast cell cycle by combining sequence, ChIP-chip and gene expression data. Lemmens et al. [] developed ReMoDiscovery to identify GRMs of the yeast cell cycle and yeast stress response by combining motif information, ChIP-chip and gene expression data. Tanay et al. [] applied a graph theoretic approach […]

library_books

Bayesian hierarchical model for transcriptional module discovery by jointly modeling gene expression and ChIP chip data

2007
BMC Bioinformatics
PMCID: 1994961
PMID: 17683565
DOI: 10.1186/1471-2105-8-283

[…] alue < 0.001). It then searches for other genes at a lower level of significance (p-value < 0.01) that are bound by those TFs and have similar expression levels to the initial gene set core (d < d0). ReMoDiscovery [] follows similar stringent and relaxed two step procedures and infers TMs from Chip-chip, motif and expression data. Module Finding Algorithm (MOFA) also uses two level p-values, but a […]

Citations

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ReMoDiscovery institution(s)
[email protected], Department of Electrical Engineering, KU Leuven, Kasteelpark Arenberg, Heverlee, Belgium; Research Group on Quantitative Psychology, Department of Psychology, KU Leuven, Tiensestraat, Leuven, Belgium; Molecular Physiology of Plants and Micro-organisms Section, Biology Department, KU Leuven, Kasteelpark Arenberg, Heverlee, Belgium; CMPG, Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg, Heverlee, Belgium
ReMoDiscovery funding source(s)
Supported by IWT projects, GBOU-SQUAD-20160; Research Council KULeuven, GOA Mefisto-666, GOA-Ambiorics, IDO genetic networks, CoE EF/05/007 SymBioSys; FWO projects, G.0413.03, and G.0241.04; IUAP V-22 (2002-2006).

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