IRegNet: an integrative Regulatory Network analysis tool for Arabidopsis thaliana. Issue 3 (10th August 2021)

• Record Type: Journal Article
• Authors: Shim, Sangrea; Park, Chung-Mo; Seo, Pil Joon
• Is Part Of: Plant physiology. Volume 187:Issue 3(2021)
• Page Start: 1292
• Page End: 1309
• Publication Date: 2021-08-10
• Subjects: Plant physiology -- Periodicals; Botany -- Periodicals; Periodicals; Electronic journals; 571.2
• DOI: 10.1093/plphys/kiab389
• Languages: English
• ISSNs: 0032-0889

Abstract

Abstract: Gene expression is delicately controlled via multilayered genetic and/or epigenetic regulatory mechanisms. Rapid development of the high-throughput sequencing (HTS) technology and its derivative methods including chromatin immunoprecipitation sequencing (ChIP-seq) and DNA affinity purification sequencing (DAP-seq) have generated a large volume of data on DNA–protein interactions (DPIs) and histone modifications on a genome-wide scale. However, the ability to comprehensively retrieve empirically validated upstream regulatory networks of genes of interest (GOIs) and genomic regions of interest (ROIs) remains limited. Here, we present i ntegrative Reg ulatory Net work (iRegNet), a web application that analyzes the upstream regulatory network for user-queried GOIs or ROIs in the Arabidopsis ( Arabidopsis thaliana ) genome. iRegNet covers the largest empirically proven DNA-binding profiles of Arabidopsis transcription factors (TFs) and non-TF proteins, and histone modifications obtained from all currently available Arabidopsis ChIP-seq and DAP-seq data. iRegNet not only catalogs upstream regulomes and epigenetic chromatin states for single-query gene/genomic region but also suggests significantly overrepresented upstream genetic regulators and epigenetic chromatin states of user-submitted multiple query genes/genomic regions. Furthermore, gene-to-gene coexpression index and protein–protein interaction information were also integrated into iRegNet for a more reliable identification of upstream regulators and realistic regulatory networks. Thus, iRegNet will help discover upstream regulators as well as molecular regulatory networks of GOI(s) and/or ROI(s), and is freely available at http://chromatindynamics.snu.ac.kr:8082/iRegNet_main . Abstract : iRegNet is a web application analyzing chromatin states and transcriptional regulatory network (CSTRN) for user-queried gene(s)- or genomic region(s)-of-interest in the Arabidopsis genome.