FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Transcription factors (TFs) are crucial regulators of gene expression.
• High-throughput sequencing methods generate vast amounts of data, necessitating advanced analytical tools.
• There is a growing need for comprehensive frameworks to infer influential TFs from ChIP-seq/ATAC-seq data.

Purpose of the Study:

• To introduce FindIT2, an R/Bioconductor package for processing and analyzing high-throughput multi-omics data.
• To provide a complete framework for annotating ChIP-seq/ATAC-seq peaks and identifying TF targets.
• To enable the inference of influential TFs using diverse data inputs.

Main Methods:

• Development of the FindIT2 R/Bioconductor package.
• Implementation of annotation and processing pipelines for ChIP-seq and ATAC-seq data.
• Integration of RNA-seq data for TF target identification.

Main Results:

• FindIT2 facilitates the annotation of ChIP-seq/ATAC-seq peaks.
• The package enables the identification of TF targets by combining ChIP-seq and RNA-seq data.
• FindIT2 allows for the inference of influential TFs from various data types.
• The tool supports species with existing genomic annotations, including non-model organisms.

Conclusions:

• FindIT2 offers a user-friendly and flexible framework for analyzing multi-omics data.
• The package generates results adaptable to the available genomic annotation richness.
• FindIT2 is cross-platform compatible and freely available under the Artistic-2.0 License via Bioconductor.