ArticlePLoS computational biology2009
A factor graph nested effects model to identify networks from genetic perturbations.
Article in PLoS computational biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
- MC EMiNEM maps the interaction landscape of the Mediator.PLoS computational biology · 2012Pooled it
- Context-Specific Nested Effects Models.Journal of computational biology : a journal of computational molecular cell biology · 2020Article
- Inferring signalling dynamics by integrating interventional with observational data.Bioinformatics (Oxford, England) · 2019Article
- Augmenting subnetwork inference with information extracted from the scientific literature.PLoS computational biology · 2019Article
- Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Review
- DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Context-Specific Nested Effects Models.Research in computational molecular biology : ... Annual International Conference, RECOMB ... : proceedings. RECOMB (Conference : 2005- ) · 2018Article
- Inferring modulators of genetic interactions with epistatic nested effects models.PLoS computational biology · 2017Article
- Article
- Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models.Bioinformatics (Oxford, England) · 2016Article
- Pathway connectivity and signaling coordination in the yeast stress-activated signaling network.Molecular systems biology · 2014Article
- Inferring host gene subnetworks involved in viral replication.PLoS computational biology · 2014Article
- Multi-omic network signatures of disease.Frontiers in genetics · 2014Article
- Considering unknown unknowns: reconstruction of nonconfoundable causal relations in biological networks.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- Perturbation biology: inferring signaling networks in cellular systems.PLoS computational biology · 2013Article
- A single source k-shortest paths algorithm to infer regulatory pathways in a gene network.Bioinformatics (Oxford, England) · 2012Article
- Evolution of domain architectures and catalytic functions of enzymes in metabolic systems.Genome biology and evolution · 2012Article
- Voltage-gated Na+ channel SCN5A is a key regulator of a gene transcriptional network that controls colon cancer invasion.Cancer research · 2010Article
- A systems-biology approach to modular genetic complexity.Chaos (Woodbury, N.Y.) · 2010Review
- How to understand the cell by breaking it: network analysis of gene perturbation screens.PLoS computational biology · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Complex phenotypes such as the transformation of a normal population of cells into cancerous tissue result from a series of molecular triggers gone awry. We describe a method that searches for a genetic network consistent with expression changes observed under the knock-down of a set of genes that share a common role in the cell, such as a disease phenotype. The method extends the Nested Effects Model of Markowetz et al. (2005) by using a probabilistic factor graph to search for a network representing interactions among these silenced genes. The method also expands the network by attaching new genes at specific downstream points, providing candidates for subsequent perturbations to further characterize the pathway. We investigated an extension provided by the factor graph approach in which the model distinguishes between inhibitory and stimulatory interactions. We found that the extension yielded significant improvements in recovering the structure of simulated and Saccharomyces cerevisae networks. We applied the approach to discover a signaling network among genes involved in a human colon cancer cell invasiveness pathway. The method predicts several genes with new roles in the invasiveness process. We knocked down two genes identified by our approach and found that both knock-downs produce loss of invasive potential in a colon cancer cell line. Nested effects models may be a powerful tool for inferring regulatory connections and genes that operate in normal and disease-related processes.
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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.