ArticleScientific reports2018
PredCRP: predicting and analysing the regulatory roles of CRP from its binding sites in Escherichia coli.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 31 citations in OpenAlex.
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- UNRAVELING CRP/cAMP-MEDIATED METABOLIC REGULATION INbioRxiv : the preprint server for biology · 2025Article
- L-Rhamnose Globally Changes the Transcriptome of Planktonic and BiofilmMicroorganisms · 2024Article
- CRP improves the survival and competitive fitness ofJournal of bacteriology · 2024Article
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- An evolutionary learning-based method for identifying a circulating miRNA signature for breast cancer diagnosis prediction.NAR genomics and bioinformatics · 2024Article
- Unleashing the Influence of cAMP Receptor Protein: The Master Switch of Bacteriocin Export inInternational journal of molecular sciences · 2023Article
- Quantitative model for genome-wide cyclic AMP receptor protein binding site identification and characteristic analysis.Briefings in bioinformatics · 2023Article
- Effects of Global and Specific DNA-Binding Proteins on Transcriptional Regulation of theInternational journal of molecular sciences · 2022Article
- Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming.PLoS computational biology · 2022Article
- Evolutionary Learning-Derived Clinical-Radiomic Models for Predicting Early Recurrence of Hepatocellular Carcinoma after Resection.Liver cancer · 2021Article
- ChIP-seq Analysis of the Global Regulator Vfr Reveals Novel Insights Into the Biocontrol AgentFrontiers in microbiology · 2021Article
- Global Regulator of Rubber Degradation in Gordonia polyisoprenivorans VH2: Identification and Involvement in the Regulation Network.Applied and environmental microbiology · 2020Article
- Metabolic perturbations in mutants of glucose transporters and their applications in metabolite production in Escherichia coli.Microbial cell factories · 2019Article
- Transcriptional regulation of fatty acid cis-trans isomerization in the solvent-tolerant soil bacterium, Pseudomonas putida F1.Environmental microbiology · 2019Article
- Identifying a miRNA signature for predicting the stage of breast cancer.Scientific reports · 2018Article
- Influence of Glucose Availability and CRP Acetylation on the Genome-Wide Transcriptional Response ofFrontiers in microbiology · 2018Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cyclic AMP receptor protein (CRP), a global regulator in Escherichia coli, regulates more than 180 genes via two roles: activation and repression. Few methods are available for predicting the regulatory roles from the binding sites of transcription factors. This work proposes an accurate method PredCRP to derive an optimised model (named PredCRP-model) and a set of four interpretable rules (named PredCRP-ruleset) for predicting and analysing the regulatory roles of CRP from sequences of CRP-binding sites. A dataset consisting of 169 CRP-binding sites with regulatory roles strongly supported by evidence was compiled. The PredCRP-model, using 12 informative features of CRP-binding sites, and cooperating with a support vector machine achieved a training and test accuracy of 0.98 and 0.93, respectively. PredCRP-ruleset has two activation rules and two repression rules derived using the 12 features and the decision tree method C4.5. This work further screened and identified 23 previously unobserved regulatory interactions in Escherichia coli. Using quantitative PCR for validation, PredCRP-model and PredCRP-ruleset achieved a test accuracy of 0.96 (=22/23) and 0.91 (=21/23), respectively. The proposed method is suitable for designing predictors for regulatory roles of all global regulators in Escherichia coli. PredCRP can be accessed at https://github.com/NctuICLab/PredCRP .
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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.