ArticleNucleic acids research2007
Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 90 citations in OpenAlex.
- Article
- Serine recombinases are conserved genetic markers of antiphage defense systems.bioRxiv : the preprint server for biology · 2025Article
- Molecular Mechanisms of Phosphate Sensing, Transport and Signalling in Streptomyces and Related Actinobacteria.International journal of molecular sciences · 2021Review
- Chemotranscriptomic Profiling Defines Drug-Specific Signatures of the Glycopeptide Antibiotics Dalbavancin, Vancomycin and Chlorobiphenyl-Vancomycin in a VanB-Type-Resistant Streptomycete.Frontiers in microbiology · 2021Article
- System-level understanding of gene expression and regulation for engineering secondary metabolite production in Streptomyces.Journal of industrial microbiology & biotechnology · 2020Review
- Article
- The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2).Nature communications · 2016Article
- Co-occurrence of analogous enzymes determines evolution of a novel (βα)8-isomerase sub-family after non-conserved mutations in flexible loop.The Biochemical journal · 2016Article
- Sequence elements upstream of the core promoter are necessary for full transcription of the capsule gene operon in Streptococcus pneumoniae strain D39.Infection and immunity · 2015Article
- Correcting for link loss in causal network inference caused by regulator interference.Bioinformatics (Oxford, England) · 2014Article
- Transcriptome dynamics-based operon prediction in prokaryotes.BMC bioinformatics · 2014Article
- Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor.Nucleic acids research · 2012Article
- The -omics Era- Toward a Systems-Level Understanding of Streptomyces.Current genomics · 2011Article
- Multimodal dynamic response of the Buchnera aphidicola pLeu plasmid to variations in leucine demand of its host, the pea aphid Acyrthosiphon pisum.Molecular microbiology · 2011Article
- Article
- Genome-wide inference of regulatory networks in Streptomyces coelicolor.BMC genomics · 2010Article
- Regulation of a novel gene cluster involved in secondary metabolite production in Streptomyces coelicolor.Journal of bacteriology · 2010Article
- Genetic classification of severe early childhood caries by use of subtracted DNA fragments from Streptococcus mutans.Journal of clinical microbiology · 2008Article
- A bistable gene switch for antibiotic biosynthesis: the butyrolactone regulon in Streptomyces coelicolor.PloS one · 2008Article
- Article
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
Abstract
Streptomyces spp. produce a variety of valuable secondary metabolites, which are regulated in a spatio-temporal manner by a complex network of inter-connected gene products. Using a compilation of genome-scale temporal transcriptome data for the model organism, Streptomyces coelicolor, under different environmental and genetic perturbations, we have developed a supervised machine-learning method for operon prediction in this microorganism. We demonstrate that, using features dependent on transcriptome dynamics and genome sequence, a support vector machines (SVM)-based classification algorithm can accurately classify >90% of gene pairs in a set of known operons. Based on model predictions for the entire genome, we verified the co-transcription of more than 250 gene pairs by RT-PCR. These results vastly increase the database of known operons in S. coelicolor and provide valuable information for exploring gene function and regulation to harness the potential of this differentiating microorganism for synthesis of natural products.
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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.