1. Главная
  2. Ресурсы
  3. Библиотечный поиск
RegulonDB version9.0: high-levelintegration of generegulation,coexpression, motifclustering and beyond Socorro Gama‐CastroHeladia SalgadoAlberto Santos-Zavaleta2015 год

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond
статья из журнала

Полный текстСтраница публикацииПубликация в OpenAlex
Аннотация: RegulonDB (http://regulondb.ccg.unam.mx) is one of the most useful and important resources on bacterial gene regulation,as it integrates the scattered scientific knowledge of the best-characterized organism, Escherichia coli K-12, in a database that organizes large amounts of data. Its electronic format enables researchers to compare their results with the legacy of previous knowledge and supports bioinformatics tools and model building. Here, we summarize our progress with RegulonDB since our last Nucleic Acids Research publication describing RegulonDB, in 2013. In addition to maintaining curation up-to-date, we report a collection of 232 interactions with small RNAs affecting 192 genes, and the complete repertoire of 189 Elementary Genetic Sensory-Response units (GENSOR units), integrating the signal, regulatory interactions, and metabolic pathways they govern. These additions represent major progress to a higher level of understanding of regulated processes. We have updated the computationally predicted transcription factors, which total 304 (184 with experimental evidence and 120 from computational predictions); we updated our position-weight matrices and have included tools for clustering them in evolutionary families. We describe our semiautomatic strategy to accelerate curation, including datasets from high-throughput experiments, a novel coexpression distance to search for 'neighborhood' genes to known operons and regulons, and computational developments.
Год издания: 2015
Авторы: Socorro Gama‐Castro, Heladia Salgado, Alberto Santos-Zavaleta, Daniela Ledezma-Tejeida, Luis Muñiz-Rascado, Jair Santiago García-Sotelo, Kevin Alquicira‐Hernández, Irma Martínez‐Flores, Lucia Pannier, Jaime A. Castro-Mondragón, Alejandra Medina-Rivera, Hilda Solano-Lira, César Bonavides-Martínez, Ernesto Pérez‐Rueda, Shirley Alquicira-Hernández, Liliana Porrón-Sotelo, Alejandra López-Fuentes, Anastasia Hernández-Koutoucheva, Víctor Del Moral-Chávez, Fabio Rinaldi, Julio Collado‐Vides
Издательство: Oxford University Press
Источник: Nucleic Acids Research
Ключевые слова: Bioinformatics and Genomic Networks, Biofuel production and bioconversion, Gene Regulatory Network Analysis
Другие ссылки: Nucleic Acids Research (PDF)
Nucleic Acids Research (HTML)
amu.hal.science (HTML)
HAL (Le Centre pour la Communication Scientifique Directe) (HTML)
Europe PMC (PubMed Central) (PDF)
Europe PMC (PubMed Central) (HTML)
PubMed Central (HTML)
PubMed (HTML)