iRegNet

iRegNet reconstructs upstream regulatory networks for Arabidopsis thaliana by integrating empirically validated DNA-binding profiles from ChIP-seq and DAP-seq with histone modification, gene-to-gene coexpression, and protein–protein interaction data to characterize upstream regulomes and epigenetic chromatin states of genes or genomic regions (GOIs/ROIs).

Key Features:

• Extensive Data Integration: Incorporates the largest collection of empirically validated DNA-binding profiles for Arabidopsis transcription factors (TFs) and non-TF proteins alongside histone modification data derived from ChIP-seq and DAP-seq datasets.
• Comprehensive Network Analysis: Provides catalogs of upstream regulomes and epigenetic chromatin states for single-query genes or genomic regions (GOIs/ROIs) and identifies significantly overrepresented upstream genetic regulators and chromatin states when multiple queries are submitted.
• Coexpression and Interaction Data: Integrates gene-to-gene coexpression indices and protein–protein interaction information to refine identification of potential regulators and support construction of regulatory networks.

Scientific Applications:

• Identification of regulatory proteins: Enables identification of key transcription factors and non-TF proteins involved in specific biological processes in Arabidopsis thaliana.
• Exploration of epigenetic regulation: Facilitates analysis of histone modification patterns and epigenetic chromatin states influencing gene regulation using ChIP-seq and DAP-seq derived data.
• Discovery of regulatory interactions and pathways: Supports discovery of novel regulatory interactions and pathways that can inform genetic engineering or breeding programs.

Methodology:

Maps DNA–protein interactions and histone modifications using ChIP-seq and DAP-seq high-throughput sequencing data to generate empirically validated DNA-binding profiles; integrates gene-to-gene coexpression indices and protein–protein interaction data to refine regulator identification and detect overrepresented upstream regulators and epigenetic chromatin states for GOIs/ROIs.