FindIT2

FindIT2 identifies influential transcription factors and their targets by integrating ChIP-seq, ATAC-seq, and RNA-seq data to analyze transcriptional regulation.

Key Features:

• Multi-Omics Data Integration: Integrates ChIP-seq, ATAC-seq, and RNA-seq datasets for combined analysis of transcriptional regulation.
• Annotation Framework: Performs peak annotation for ChIP-seq and ATAC-seq to locate TF binding sites and regulatory regions.
• Target Identification: Identifies transcription factor targets by combining ChIP-seq peak information with RNA-seq expression data.
• Influence Inference: Infers influential transcription factors from diverse data inputs to prioritize TFs impacting regulation.
• Species Flexibility: Leverages Bioconductor annotation capabilities to support analyses across multiple species, including non-model organisms.

Scientific Applications:

• Gene regulatory network analysis: Reconstruction and analysis of TF-driven regulatory interactions using integrated multi-omics data.
• Transcription factor target discovery: Identification of direct TF targets through combined ChIP-seq and RNA-seq evidence.
• Chromatin accessibility and TF binding studies: Analysis of ATAC-seq and ChIP-seq peaks to link chromatin state with TF occupancy.
• Developmental biology: Dissection of complex regulatory networks underlying developmental processes.
• Disease mechanism research: Elucidation of TF-driven gene expression changes relevant to disease contexts.
• Evolutionary genomics: Comparative regulatory analyses across species with varying annotation completeness.

Methodology:

Processes high-throughput ChIP-seq and ATAC-seq with peak annotation, integrates these data with RNA-seq to identify TF targets, and applies inference methods to prioritize influential transcription factors while using Bioconductor annotation resources for species-specific mapping.