ArticleBioinformatics (Oxford, England)2011
Physical Module Networks: an integrative approach for reconstructing transcription regulation.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 44 citations in OpenAlex.
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- Unveiling the complexity of transcription factor networks in hematopoietic stem cells: implications for cell therapy and hematological malignancies.Frontiers in oncology · 2023Review
- LIGHT (TNFSF14) Costimulation Enhances Myeloid Cell Activation and Antitumor Immunity in the Setting of PD-1/PD-L1 and TIGIT Checkpoint Blockade.Journal of immunology (Baltimore, Md. : 1950) · 2022Article
- Fusion of single-cell transcriptome and DNA-binding data, for genomic network inference in cortical development.BMC bioinformatics · 2021Article
- Reprogramming of regulatory network using expression uncovers sex-specific gene regulation in Drosophila.Nature communications · 2018Article
- Adjustment of dendritic cells to the breast-cancer microenvironment is subset specific.Nature immunology · 2018Article
- An approach to infer putative disease-specific mechanisms using neighboring gene networks.Bioinformatics (Oxford, England) · 2017Article
- On the performance of de novo pathway enrichment.NPJ systems biology and applications · 2017Article
- Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens.PLoS computational biology · 2016Article
- Integrative multi-omics module network inference with Lemon-Tree.PLoS computational biology · 2015Article
- Pathway connectivity and signaling coordination in the yeast stress-activated signaling network.Molecular systems biology · 2014Article
- An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development.PLoS genetics · 2014Article
- Inferring host gene subnetworks involved in viral replication.PLoS computational biology · 2014Article
- Democratizing systems immunology with modular transcriptional repertoire analyses.Nature reviews. Immunology · 2014Review
- Molecular mechanisms of system responses to novel stimuli are predictable from public data.Nucleic acids research · 2014Article
- Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways.Cancer informatics · 2014Review
- Nanowire-mediated delivery enables functional interrogation of primary immune cells: application to the analysis of chronic lymphocytic leukemia.Nano letters · 2012Article
- Application of a systems approach to study developmental gene regulation.Biophysical reviews · 2012Review
- Identification of aberrant pathways and network activities from high-throughput data.Briefings in bioinformatics · 2012Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
motivationDeciphering the complex mechanisms by which regulatory networks control gene expression remains a major challenge. While some studies infer regulation from dependencies between the expression levels of putative regulators and their targets, others focus on measured physical interactions.
resultsHere, we present Physical Module Networks, a unified framework that combines a Bayesian model describing modules of co-expressed genes and their shared regulation programs, and a physical interaction graph, describing the protein-protein interactions and protein-DNA binding events that coherently underlie this regulation. Using synthetic data, we demonstrate that a Physical Module Network model has similar recall and improved precision compared to a simple Module Network, as it omits many false positive regulators. Finally, we show the power of Physical Module Networks to reconstruct meaningful regulatory pathways in the genetically perturbed yeast and during the yeast cell cycle, as well as during the response of primary epithelial human cells to infection with H1N1 influenza. AVAILABILITY: The PMN software is available, free for academic use at http://www.compbio.cs.huji.ac.il/PMN/. CONTACT: aregev@broad.mit.edu; nirf@cs.huji.ac.il.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.