FFLtool: a web server for transcription factor and miRNA feed forward loop analysis in human.

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• Transcription factors (TFs) and microRNAs (miRNAs) are key regulators of gene expression at transcriptional and post-transcriptional levels, respectively.
• Understanding the intricate cross-talk between TFs, miRNAs, and their target genes is crucial for deciphering complex molecular regulatory networks.

Purpose of the Study:

• To develop a computational tool, FFLtool, for the identification of potential feed-forward loops (FFLs) involving TFs, miRNAs, and their targets in the human genome.
• To provide a comprehensive resource for researchers to investigate gene regulatory mechanisms and their implications in biological processes and diseases.

Main Methods:

• Integration of extensive TF-target and miRNA-target regulatory data.
• Development of an 'FFL Analysis' module to detect FFLs and internal regulatory networks within user-defined gene sets.
• Implementation of a 'Browse FFLs' module to visualize FFLs in human cancers, highlighting differentially expressed TFs and miRNAs.

Main Results:

• FFLtool successfully identifies potential TF-miRNA-target FFLs and associated regulatory networks.
• The tool offers multiple levels of evidence to assess the reliability of predicted FFLs.
• Enrichment functions are provided for co-targeted genes regulated by the same TF and miRNA, offering deeper mechanistic insights.

Conclusions:

• FFLtool serves as a valuable web-based resource for the systematic detection and analysis of feed-forward loops in human gene regulation.
• The tool facilitates the study of complex gene expression regulation, contributing to a better understanding of molecular mechanisms underlying biological processes and diseases, particularly in cancer research.