CiiiDER: A tool for predicting and analysing transcription factor binding sites

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• High-throughput genomic, transcriptomic, and epigenomic data offer deep insights into cellular transcriptome regulation.
• Research has progressed from identifying gene expression patterns to elucidating regulatory signaling pathways.
• Over 1,000 transcription factors (TFs) in vertebrates regulate gene expression, but identifying their specific roles is challenging.

Purpose of the Study:

• To present CiiiDER, an integrated computational toolkit for transcription factor binding analysis.
• To provide a user-friendly tool for predicting transcription factor binding sites (TFBSs) across various genomic regions.
• To enable the identification of regulatory pathways involved in pathophysiological processes.

Main Methods:

• CiiiDER is a Java-based computational toolkit, ensuring cross-platform compatibility.
• It features an intuitive graphical user interface (GUI) with interactive visualizations.
• The toolkit predicts TFBSs in regulatory regions (promoters, enhancers) and performs enrichment analysis against custom background sets.

Main Results:

• CiiiDER accurately predicts transcription factor binding sites (TFBSs) across diverse species.
• The toolkit facilitates the identification of significantly over- or under-represented TFs in specific gene sets.
• Enrichment analysis aids in elucidating regulatory pathways controlling genes of pathophysiological importance.

Conclusions:

• CiiiDER is an accessible and versatile tool for transcription factor binding analysis.
• It empowers researchers to investigate gene regulation and identify disease-associated pathways.
• The toolkit enhances the understanding of complex biological systems through computational prediction.