RegulonDB

RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. RegulonDB (http://regulondb.ccg.unam.mx/) is the primary reference database offering curated knowledge of the transcriptional regulatory network of Escherichia coli K12, currently the best-known electronically encoded database of the genetic regulatory network of any free-living organism. This paper summarizes the improvements, new biology and new features available in version 6.0. Curation of original literature is, from now on, up to date for every new release. All the objects are supported by their corresponding evidences, now classified as strong or weak. Transcription factors are classified by origin of their effectors and by gene ontology class. We have now computational predictions for σ54 and five different promoter types of the σ70 family, as well as their corresponding −10 and −35 boxes. In addition to those curated from the literature, we added about 300 experimentally mapped promoters coming from our own high-throughput mapping efforts. RegulonDB v.6.0 now expands beyond transcription initiation, including RNA regulatory elements, specifically riboswitches, attenuators and small RNAs, with their known associated targets. The data can be accessed through overviews of correlations about gene regulation. RegulonDB associated original literature, together with more than 4000 curation notes, can now be searched with the Textpresso text mining engine


References in zbMATH (referenced in 51 articles )

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  1. Krishnan, Jeyashree; Torabi, Reza; Schuppert, Andreas; Di Napoli, Edoardo: A modified Ising model of Barabási-Albert network with gene-type spins (2020)
  2. Sanguinetti, Guido (ed.); Huynh-Thu, Vân Anh (ed.): Gene regulatory networks. Methods and protocols (2019)
  3. Savir, Yonatan; Kagan, Jacob; Tlusty, Tsvi: Binding of transcription factors adapts to resolve information-energy tradeoff (2016)
  4. Tan, Heli; Yuan, Zhanjiang; Zhang, Jiajun; Zhou, Tianshou: Characteristics of promoter architecture-dependent expression noise and bursting kinetics (2016)
  5. Fioretto, Ferdinando; Dovier, Agostino; Pontelli, Enrico: Constrained community-based gene regulatory network inference (2015)
  6. Lopes, Fabrício M.; Martins, David C.; Barrera, Junior; Cesar, Roberto M.: A feature selection technique for inference of graphs from their known topological properties: revealing scale-free gene regulatory networks (2014) ioport
  7. Rosen, Yonatan; Louzoun, Yoram: Directionality of real world networks as predicted by path length in directed and undirected graphs (2014)
  8. Sun, Yixiang; Du, Haifeng; Gong, Maoguo; Ma, Lijia; Wang, Shanfeng: Fast computing global structural balance in signed networks based on memetic algorithm (2014)
  9. Bernot, Gilles; Comet, Jean-Paul; Richard, Adrien; Chaves, Madalena; Gouzé, Jean-Luc; Dayan, Frédéric: Modeling and analysis of gene regulatory networks (2013)
  10. Bodaker, Matan; Louzoun, Yoram; Mitrani, Eduardo: Mathematical conditions for induced cell differentiation and trans-differentiation in adult cells (2013)
  11. Mahdevar, Ghasem; Sadeghi, Mehdi; Nowzari-Dalini, Abbas: Transcription factor binding sites detection by using alignment-based approach (2012)
  12. Martins, Leonardo; Mäkelä, Jarno; Häkkinen, Antti; Kandhavelu, Meenakshisundaram; Yli-Harja, Olli; Fonseca, José M.; Ribeiro, Andre S.: Dynamics of transcription of closely spaced promoters in \textitEscherichiacoli, one event at a time (2012)
  13. Roverato, Alberto; Castelo, Robert: Learning undirected graphical models from multiple datasets with the generalized non-rejection rate (2012) ioport
  14. Wei, Peng; Pan, Wei: Bayesian joint modeling of multiple gene networks and diverse genomic data to identify target genes of a transcription factor (2012)
  15. de Avila e Silva, Scheila; Echeverrigaray, Sergio; Gerhardt, Günther J. L.: BacPP: bacterial promoter prediction -- a tool for accurate sigma-factor specific assignment in enterobacteria (2011)
  16. Gama-Castro, Socorro; Salgado, Heladia; Peralta-Gil, Martín; Santos-Zavaleta, Alberto; Muñiz-Rascado, Luis; Solano-Lira, Hilda; Jiménez-Jacinto, Verónica; Weiss, Verena; García-Sotelo, Jair S.; López-Fuentes, Alejandra; Porrón-Sotelo, Liliana; Alquicira-Hernández, Shirley; Medina-Rivera, Alejandra; Martínez-Flores, Irma; Alquicira-Hernández, Kevin; Martínez-Adame, Ruth; Bonavides-Martínez, César; Miranda-Ríos, Juan; Huerta, Araceli M.; Mendoza-Vargas, Alfredo; Collado-Torres, Leonardo; Taboada, Blanca; Vega-Alvarado, Leticia; Olvera, Maricela; Olvera, Leticia; Grande, Ricardo; Morett, Enrique; Collado-Vides, Julio: Regulondb version 7.0: transcriptional regulation of \textitescherichiacoli K-12 integrated within genetic sensory response units (Gensor units) (2011) ioport
  17. Goñi-Moreno, Angel; Redondo-Nieto, Miguel; Arroyo, Fernando; Castellanos, Juan: Biocircuit design through engineering bacterial logic gates (2011) ioport
  18. Mabrouki, Mbarka; Aiguier, Marc; Comet, Jean-Paul; Le Gall, Pascale; Richard, Adrien: Embedding of biological regulatory networks and property preservation (2011)
  19. Roverato, Alberto; Di Lascio, F. Marta L.: Wilks’ (\Lambda) dissimilarity measures for gene clustering: an approach based on the identification of transcription modules (2011)
  20. Cerulo, Luigi; Elkan, Charles; Ceccarelli, Michele: Learning gene regulatory networks from only positive and unlabeled data (2010) ioport

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