RESUMEN
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.
Asunto(s)
Bases de Datos Genéticas , Escherichia coli K12 , Regulación Bacteriana de la Expresión Génica , Biología Computacional/métodos , Escherichia coli K12/genética , Internet , Transcripción GenéticaRESUMEN
Chronic Obstructive Pulmonary Disease (COPD) and Idiopathic Pulmonary Fibrosis (IPF) have contrasting clinical and pathological characteristics and interesting whole-genome transcriptomic profiles. However, data from public repositories are difficult to reprocess and reanalyze. Here, we present PulmonDB, a web-based database (http://pulmondb.liigh.unam.mx/) and R library that facilitates exploration of gene expression profiles for these diseases by integrating transcriptomic data and curated annotation from different sources. We demonstrated the value of this resource by presenting the expression of already well-known genes of COPD and IPF across multiple experiments and the results of two differential expression analyses in which we successfully identified differences and similarities. With this first version of PulmonDB, we create a new hypothesis and compare the two diseases from a transcriptomics perspective.
Asunto(s)
Bases de Datos Genéticas , Redes Reguladoras de Genes , Fibrosis Pulmonar Idiopática/genética , Enfermedad Pulmonar Obstructiva Crónica/genética , Curaduría de Datos , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Humanos , Internet , Secuenciación del ExomaRESUMEN
MOTIVATION: Identifying disease-causing variants from exome sequencing projects remains a challenging task that often requires bioinformatics expertise. Here we describe a user-friendly graphical application that allows medical professionals and bench biologists to prioritize and visualize genetic variants from human exome sequencing data. RESULTS: We have implemented VCF/Plotein, a graphical, fully interactive web application able to display exome sequencing data in VCF format. Gene and variant information is extracted from Ensembl. Cross-referencing with external databases and application-based gene and variant filtering have also been implemented. All data processing is done locally by the user's CPU to ensure the security of patient data. AVAILABILITY AND IMPLEMENTATION: Freely available on the web at https://vcfplotein.liigh.unam.mx. Website implemented in JavaScript using the Vue.js framework, with all major browsers supported. Source code freely available for download at https://github.com/raulossio/VCF-plotein. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.