Reconstruction and Analysis of the Evolution of Modular Transcriptional Regulatory Programs Using Arboretum.

Sara A Knaack, Dawn A Thompson, Sushmita Roy

Abstract read

In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed

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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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4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Sara A KnaackWisconsin Institute for Discovery, University of Wisconsin at Madison, Madison, WI, USA.

Dawn A ThompsonBroad Institute of MIT and Harvard, Cambridge, MA, USA.

Sushmita RoyWisconsin Institute for Discovery, University of Wisconsin at Madison, Madison, WI, USA. sroy@biostat.wisc.edu.

Funding

Research Training for Computation and Informatics in Biology and MedicineT15LM007359 · NLM · UNIVERSITY OF WISCONSIN-MADISON · PI Mark W. Craven, Colin Noel Dewey · 2002 to 2026

$22.6M

Genome-wide analysis of regulated chromosomal domains: From mechanisms to cancerR01CA119176 · NCI · WEIZMANN INSTITUTE OF SCIENCE · PI REGEV, AVIV, SEGAL, ERAN · 2006 to 2015

$3.7M

NCI NIH HHS 2R01CA119176-01NCI NIH HHS R01 CA119176NLM NIH HHS 5T15LM007359NLM NIH HHS T15 LM007359

6 · The paper itself

Abstract

Comparative functional genomics aims to measure and compare genome-wide functional data such as transcriptomes, proteomes, and epigenomes across multiple species to study the conservation and divergence patterns of such quantitative measurements. However, computational methods to systematically compare these quantitative genomic profiles across multiple species are in their infancy. We developed Arboretum, a novel algorithm to identify modules of co-expressed genes and trace their evolutionary history across multiple species from a complex phylogeny. To interpret the results from Arboretum we developed several measures to examine the extent of conservation and divergence in modules and their relationship to species lifestyle, cis-regulatory elements, and gene duplication. We applied Arboretum to study the evolution of modular transcriptional regulatory programs controlling transcriptional response to different environmental stresses in the yeast Ascomycota phylogeny. We found that modules of similar patterns of expression captured the transcriptional responses to different stresses across species; however, the genes exhibiting these patterns were not the same. Divergence in module membership was associated with changes in lifestyle and specific clades and that gene duplication was a major factor contributing to the divergence of module membership.

Indexed as

Gene Regulatory NetworksPhylogenyAlgorithmsComputational BiologyGene DuplicationGene Expression Regulation, FungalSaccharomyces cerevisiaeTranscription FactorsTranscription FactorsArboretumEvolutionGaussian mixture model (GMM)Gene treeMulti-clusteringPhylogenyRegulatory networksTranscriptional module s

Identifiers

PMID26483033

DOI10.1007/978-1-4939-3079-1_21

PMCPMC5689457

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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.