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. 2024 Jan 5;52(D1):D255-D264.
doi: 10.1093/nar/gkad1072.

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12

Heladia Salgado  1 , Socorro Gama-Castro  1 , Paloma Lara  1 , Citlalli Mejia-Almonte  1 , Gabriel Alarcón-Carranza  1 , Andrés G López-Almazo  1 , Felipe Betancourt-Figueroa  1 , Pablo Peña-Loredo  1 , Shirley Alquicira-Hernández  1 , Daniela Ledezma-Tejeida  1 , Lizeth Arizmendi-Zagal  1 , Francisco Mendez-Hernandez  1 , Ana K Diaz-Gomez  1 , Elizabeth Ochoa-Praxedis  1 , Luis J Muñiz-Rascado  1 , Jair S García-Sotelo  2 , Fanny A Flores-Gallegos  1 , Laura Gómez  3   4 , César Bonavides-Martínez  1 , Víctor M Del Moral-Chávez  1 , Alfredo J Hernández-Alvarez  1 , Alberto Santos-Zavaleta  5 , Salvador Capella-Gutierrez  6 , Josep Lluis Gelpi  7   8 , Julio Collado-Vides  1   8   9
Affiliations

RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12

Heladia Salgado et al. Nucleic Acids Res. .

Abstract

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrieval and accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0 can be accessed at https://regulondb.ccg.unam.mx.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Class diagram of genetic regulation and datamarts in RegulonDB. (A) Class model of gene regulation. In this diagram, each box represents an entity or biological concept, and the lines between them indicate cardinality relationships. The notation ‘1..*’ represents a relationship of one or more elements, while ‘0..*’ indicates a relationship of zero or more elements, that is, optional elements. (B) Class diagram of the datamarts in RegulonDB. These datamarts integrate one or more biological entities from the class model presented in panel a. This graph also describes the RegulonDB Web page navigation.
Figure 2.
Figure 2.
Illustration of the apollo sandbox interface to perform searches in RegulonDB using Web services. At point 1, in the query section, users can select the attributes they wish to visualize. At point 2, the query results are displayed based on the applied filters. At the final point, marked as 3, all available Web services are listed.
Figure 3.
Figure 3.
illustrates the main Web components utilized in creating the five key Web pages mentioned: (1) the query box; (2) the catalog of elements where users can browse and search for specific items; (3) the object identification properties component; (4) the graphical representation component of the queried object; (5) the navigation menu for moving between sections of the page; (6) the related tools component and (7) the component describing object specific details.
See this image and copyright information in PMC

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