ArticleGenome research2013
Arboretum: reconstruction and analysis of the evolutionary history of condition-specific transcriptional modules.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
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- Accounting for cis-regulatory constraint prioritizes genes likely to affect species-specific traits.Genome biology · 2023Article
- Modular derivation of diverse, regionally discrete human posterior CNS neurons enables discovery of transcriptomic patterns.Science advances · 2022Article
- Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes.mBio · 2022Article
- Enabling Studies of Genome-Scale Regulatory Network Evolution in Large Phylogenies with MRTLE.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Single cell gene regulatory networks in plants: Opportunities for enhancing climate change stress resilience.Plant, cell & environment · 2021Review
- A network-based comparative framework to study conservation and divergence of proteomes in plant phylogenies.Nucleic acids research · 2021Article
- Evolution of regulatory networks associated with traits under selection in cichlids.Genome biology · 2021Article
- Comparative Analyses of Gene Co-expression Networks: Implementations and Applications in the Study of Evolution.Frontiers in genetics · 2021Review
- Paralogs in the PKA Regulon Traveled Different Evolutionary Routes to Divergent Expression in Budding Yeast.Frontiers in fungal biology · 2021Article
- Prediction pipeline for discovery of regulatory motifs associated with Brugia malayi molting.PLoS neglected tropical diseases · 2020Article
- Model-based clustering of multi-tissue gene expression data.Bioinformatics (Oxford, England) · 2020Article
- Ancestral reconstruction of protein interaction networks.PLoS computational biology · 2019Article
- Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development.Cell systems · 2019Article
- Repeated Cis-Regulatory Tuning of a Metabolic Bottleneck Gene during Evolution.Molecular biology and evolution · 2018Article
- Comparative Transcriptomics Highlights New Features of the Iron Starvation Response in the Human PathogenFrontiers in microbiology · 2018Article
- The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi.PLoS genetics · 2017Article
- Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes.Genome research · 2017Article
- Inference and Evolutionary Analysis of Genome-Scale Regulatory Networks in Large Phylogenies.Cell systems · 2017Article
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10 authors.
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Abstract
Comparative functional genomics studies the evolution of biological processes by analyzing functional data, such as gene expression profiles, across species. A major challenge is to compare profiles collected in a complex phylogeny. Here, we present Arboretum, a novel scalable computational algorithm that integrates expression data from multiple species with species and gene phylogenies to infer modules of coexpressed genes in extant species and their evolutionary histories. We also develop new, generally applicable measures of conservation and divergence in gene regulatory modules to assess the impact of changes in gene content and expression on module evolution. We used Arboretum to study the evolution of the transcriptional response to heat shock in eight species of Ascomycota fungi and to reconstruct modules of the ancestral environmental stress response (ESR). We found substantial conservation in the stress response across species and in the reconstructed components of the ancestral ESR modules. The greatest divergence was in the most induced stress, primarily through module expansion. The divergence of the heat stress response exceeds that observed in the response to glucose depletion in the same species. Arboretum and its associated analyses provide a comprehensive framework to systematically study regulatory evolution of condition-specific responses.
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