ArticleNucleic acids research2014
Inference of sigma factor controlled networks by using numerical modeling applied to microarray time series data of the germinating prokaryote.
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 13 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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
13 citing papers in PubMed, 20 citations in OpenAlex.
- SMC ensures efficient chromosome replication and oriC positioning during Streptomyces spore germination.Scientific reports · 2026Article
- Optimization of Constitutive Promoters Using a Promoter-Trapping Vector inInternational journal of molecular sciences · 2023Article
- Cross-Recognition of Promoters by the Nine SigB Homologues Present inInternational journal of molecular sciences · 2021Article
- Defining the regulon of genes controlled by σMolecular microbiology · 2019Article
- Unraveling Nutritional Regulation of Tacrolimus Biosynthesis inAntibiotics (Basel, Switzerland) · 2018Review
- Genexpi: a toolset for identifying regulons and validating gene regulatory networks using time-course expression data.BMC bioinformatics · 2018Article
- Streptomyces coelicolor strains lacking polyprenol phosphate mannose synthase and protein O-mannosyl transferase are hyper-susceptible to multiple antibiotics.Microbiology (Reading, England) · 2018Article
- Secondary Metabolites Produced during the Germination ofFrontiers in microbiology · 2017Article
- A Waking Review: Old and Novel Insights into the Spore Germination inFrontiers in microbiology · 2017Review
- Genome-wide identification and characterization of reference genes with different transcript abundances for Streptomyces coelicolor.Scientific reports · 2015Article
- Genome-wide identification and evaluation of constitutive promoters in streptomycetes.Microbial cell factories · 2015Article
- Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor.BMC genomics · 2014Article
- Small non-coding RNAs in streptomycetes.RNA biology · 2014Review
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A computational model of gene expression was applied to a novel test set of microarray time series measurements to reveal regulatory interactions between transcriptional regulators represented by 45 sigma factors and the genes expressed during germination of a prokaryote Streptomyces coelicolor. Using microarrays, the first 5.5 h of the process was recorded in 13 time points, which provided a database of gene expression time series on genome-wide scale. The computational modeling of the kinetic relations between the sigma factors, individual genes and genes clustered according to the similarity of their expression kinetics identified kinetically plausible sigma factor-controlled networks. Using genome sequence annotations, functional groups of genes that were predominantly controlled by specific sigma factors were identified. Using external binding data complementing the modeling approach, specific genes involved in the control of the studied process were identified and their function suggested.
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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.