ArticleEURASIP journal on bioinformatics & systems biology2009
Reconstructing generalized logical networks of transcriptional regulation in mouse brain from temporal gene expression data.
Article in EURASIP journal on bioinformatics & systems biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A graph theoretical approach to experimental prioritization in genome-scale investigations.Mammalian genome : official journal of the International Mammalian Genome Society · 2024Article
- Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.PLoS computational biology · 2017Article
- Constrained inference of protein interaction networks for invadopodium formation in cancer.IET systems biology · 2016Article
- ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion.Nucleic acids research · 2015Article
- Hunting complex differential gene interaction patterns across molecular contexts.Nucleic acids research · 2014Article
- Harnessing diversity towards the reconstructing of large scale gene regulatory networks.PLoS computational biology · 2013Article
- Effect of rainfall-induced soil geochemistry dynamics on grassland soil microbial communities.Applied and environmental microbiology · 2012Article
- Wisdom of crowds for robust gene network inference.Nature methods · 2012Article
- A review of modeling techniques for genetic regulatory networks.Journal of medical signals and sensors · 2012Article
- Treatment- and population-dependent activity patterns of behavioral and expression QTLs.PloS one · 2012Article
- Ckmeans.1d.dp: OptimalThe R journal · 2011Article
- The complexity of alcohol drinking: studies in rodent genetic models.Behavior genetics · 2010Review
- A method for mapping intralocus interactions influencing excessive alcohol drinking.Mammalian genome : official journal of the International Mammalian Genome Society · 2010Article
- Comparative Generalized Logic Modeling Reveals Differential Gene Interactions during Cell Cycle Exit inGI-Edition. Proceedings · 2009Article
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
Gene expression time course data can be used not only to detect differentially expressed genes but also to find temporal associations among genes. The problem of reconstructing generalized logical networks to account for temporal dependencies among genes and environmental stimuli from transcriptomic data is addressed. A network reconstruction algorithm was developed that uses statistical significance as a criterion for network selection to avoid false-positive interactions arising from pure chance. The multinomial hypothesis testing-based network reconstruction allows for explicit specification of the false-positive rate, unique from all extant network inference algorithms. The method is superior to dynamic Bayesian network modeling in a simulation study. Temporal gene expression data from the brains of alcohol-treated mice in an analysis of the molecular response to alcohol are used for modeling. Genes from major neuronal pathways are identified as putative components of the alcohol response mechanism. Nine of these genes have associations with alcohol reported in literature. Several other potentially relevant genes, compatible with independent results from literature mining, may play a role in the response to alcohol. Additional, previously unknown gene interactions were discovered that, subject to biological verification, may offer new clues in the search for the elusive molecular mechanisms of alcoholism.
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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.