ArticleNucleic acids research2014
A high-resolution network model for global gene regulation in Mycobacterium tuberculosis.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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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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Who cites it
37 citing papers in PubMed, 69 citations in OpenAlex.
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- Predicting fitness inFrontiers in tuberculosis · 2025Article
- MtrA modulates Mycobacterium tuberculosis cell division in host microenvironments to mediate intrinsic resistance and drug tolerance.Cell reports · 2023Article
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- Transcriptome signature of cell viability predicts drug response and drug interaction inCell reports methods · 2021Article
- Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME.NPJ systems biology and applications · 2021Article
- Predictive regulatory and metabolic network models for systems analysis of Clostridioides difficile.Cell host & microbe · 2021Article
- Expression Dysregulation as a Mediator of Fitness Costs in Antibiotic Resistance.Antimicrobial agents and chemotherapy · 2021Article
- A systems-level gene regulatory network model for Plasmodium falciparum.Nucleic acids research · 2021Article
- History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications.Frontiers in physiology · 2021Review
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- System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster.Scientific reports · 2019Article
- It is time to apply biclustering: a comprehensive review of biclustering applications in biological and biomedical data.Briefings in bioinformatics · 2019Review
- Comparative label-free lipidomic analysis of Mycobacterium tuberculosis during dormancy and reactivation.Scientific reports · 2019Article
- Path-seq identifies an essential mycolate remodeling program for mycobacterial host adaptation.Molecular systems biology · 2019Article
- Translational regulation in mycobacteria and its implications for pathogenicity.Nucleic acids research · 2018Review
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
Abstract
The resilience of Mycobacterium tuberculosis (MTB) is largely due to its ability to effectively counteract and even take advantage of the hostile environments of a host. In order to accelerate the discovery and characterization of these adaptive mechanisms, we have mined a compendium of 2325 publicly available transcriptome profiles of MTB to decipher a predictive, systems-scale gene regulatory network model. The resulting modular organization of 98% of all MTB genes within this regulatory network was rigorously tested using two independently generated datasets: a genome-wide map of 7248 DNA-binding locations for 143 transcription factors (TFs) and global transcriptional consequences of overexpressing 206 TFs. This analysis has discovered specific TFs that mediate conditional co-regulation of genes within 240 modules across 14 distinct environmental contexts. In addition to recapitulating previously characterized regulons, we discovered 454 novel mechanisms for gene regulation during stress, cholesterol utilization and dormancy. Significantly, 183 of these mechanisms act uniquely under conditions experienced during the infection cycle to regulate diverse functions including 23 genes that are essential to host-pathogen interactions. These and other insights underscore the power of a rational, model-driven approach to unearth novel MTB biology that operates under some but not all phases of infection.
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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.