Cited by 268Gene Regulatory Network AnalysisBioinformatics and Genomic NetworksFungal and yeast genetics research

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Passing Messages between Biological Networks to Refine Predicted Interactions

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Glass, Kimberly, Huttenhower, Curtis, Quackenbush, John, Yuan, Guo-Cheng·2013·PLoS ONE

DOI 10.1371/journal.pone.0064832PMC PMC3669401

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Abstract

Regulatory network reconstruction is a fundamental problem in computational biology. There are significant limitations to such reconstruction using individual datasets, and increasingly people attempt to construct networks using multiple, independent datasets obtained from complementary sources, but methods for this integration are lacking. We developed PANDA (Passing Attributes between Networks for Data Assimilation), a message-passing model using multiple sources of information to predict regulatory relationships, and used it to integrate protein-protein interaction, gene expression, and sequence motif data to reconstruct genome-wide, condition-specific regulatory networks in yeast as a model. The resulting networks were not only more accurate than those produced using individual data sets and other existing methods, but they also captured information regarding specific biological mechanisms and pathways that were missed using other methodologies. PANDA is scalable to higher eukaryotes, applicable to specific tissue or cell type data and conceptually generalizable to include a variety of regulatory, interaction, expression, and other genome-scale data. An implementation of the PANDA algorithm is available at www.sourceforge.net/projects/panda-net.

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Additional file 5 of Gene regulatory networks reveal sex difference in lung adenocarcinoma
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Additional file 6 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
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Additional file 16 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
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Additional file 3 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
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Additional file 7 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
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Additional file 19 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
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Additional file 12 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
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Additional file 13 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
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Additional file 3 of Gene regulatory networks reveal sex difference in lung adenocarcinoma
Saha, E., Guebila, M. B., Fanfani, V., Fischer, J., Shutta, K. H., Mandros, P., DeMeo, D. L., Quackenbush, J. F., & Lopes‐Ramos, C. M. (2024) · Figshare · doi:10.6084/m9.figshare.26758201
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Additional file 10 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
Fisher, J. L., Clark, A. D., Jones, E. F., & Lasseigne, B. N. (2024) · Figshare · doi:10.6084/m9.figshare.26658772
Additional file 3 of Biologically informed NeuralODEs for genome-wide regulatory dynamics
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Additional file 11 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
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Additional file 21 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
Fisher, J. L., Clark, A. D., Jones, E. F., & Lasseigne, B. N. (2024) · Figshare · doi:10.6084/m9.figshare.26658808
Additional file 2 of Gene regulatory networks reveal sex difference in lung adenocarcinoma
Saha, E., Guebila, M. B., Fanfani, V., Fischer, J., Shutta, K. H., Mandros, P., DeMeo, D. L., Quackenbush, J. F., & Lopes‐Ramos, C. M. (2024) · Figshare · doi:10.6084/m9.figshare.26758198
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Additional file 18 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
Fisher, J. L., Clark, A. D., Jones, E. F., & Lasseigne, B. N. (2024) · Figshare · doi:10.6084/m9.figshare.26658799
Additional file 8 of Sex-biased gene expression and gene-regulatory networks of sex-biased adverse event drug targets and drug metabolism genes
Fisher, J. L., Clark, A. D., Jones, E. F., & Lasseigne, B. N. (2024) · Figshare · doi:10.6084/m9.figshare.26658766
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Additional file 7 of Gene regulatory networks reveal sex difference in lung adenocarcinoma
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FAIRsharing record for: Gene Regulatory Network Database
FAIRsharing Team, Guebila, M. B., & Guebila, M. B. (2022) · FAIRsharing.org · doi:10.25504/fairsharing.9f8852

Authors: Glass, K., Huttenhower, C., Quackenbush, J., & Yuan, G.-C.
Affiliations: Harvard University (US)
Corresponding author: Yuan, Guo-Cheng
ORCID: Glass, Kimberly
Huttenhower, Curtis
Quackenbush, John
Yuan, Guo-Cheng
Venue: PLoS ONE
Publisher: Public Library of Science (PLoS)
Published: 2013-05-31
Volume: 8
Issue: 5
Pages: e64832
ISSN: 1932-6203 (ISSN-L)
DOI: 10.1371/journal.pone.0064832
PMC: PMC3669401
OpenAlex: W2020672230
Cited by: 266
References: 64
Citations by year: 2026: 24 · 2025: 26 · 2024: 56 · 2023: 22 · 2022: 24 · 2021: 29 · 2020: 24 · 2019: 15 · 2018: 11 · 2017: 12 · 2016: 12 · 2015: 7 · 2014: 4
FWCI: 3.44
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (unspecified)
Locations: PLoS ONE (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, other-oa)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Figshare (submittedVersion, cc-by)
Funders: National Science Foundation (1053486)
National Institutes of Health (5r01hl111759-04)
National Heart, Lung, and Blood Institute (R01-HL111759, P01HL105339)
Division of Biological Infrastructure (DBI-1053486)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Keywords: regulatory network reconstruction, data integration, message passing, protein-protein interaction, gene expression, sequence motifs, yeast, genome-scale data, network prediction
MeSH terms: Algorithms, Computer Simulation, Models, Biological, Saccharomyces cerevisiae, Reproducibility of Results, Signal Transduction, Gene Regulatory Networks, Protein Interaction Maps

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Passing Messages between Biological Networks to Refine Predicted Interactions

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