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MAGNETIC: a web server to fetch gene network based on motif distribution in promoters
Atreyi Chakraborty1, Saksham Srimali1, Rohan Topno1
1Department of Biology, Indian Institute of Science Education and Research, Pune, Maharashtra 411008, India.
Nucleic Acids Research
|May 14, 2025
Summary
The MAGNETIC web server identifies gene regulatory networks by analyzing motif abundance in human gene promoters. This tool helps discover gene connections and understand gene regulation, aiding in identifying potential protein binding sites.
Area of Science:
- Genomics
- Bioinformatics
- Systems Biology
Background:
- Understanding gene regulation is crucial for deciphering complex biological processes.
- Identifying correlations in gene promoter regions can reveal functional relationships between genes.
- Existing tools may not comprehensively link motif abundance to gene regulatory network construction.
Purpose of the Study:
- To introduce MAGNETIC, a web server for searching the human genome for correlations between gene promoter regions based on motif abundance.
- To enable the discovery and determination of gene regulatory networks.
- To provide insights into gene regulation and function through network analysis.
Main Methods:
- Developed the MAGNETIC web server to analyze the human genome.
- Correlated the abundance of 5/6-mer motifs in gene promoters (1, 2, or 6 kb upstream of the gene start site).
- Linked genes with similar motif abundances to form gene regulatory networks.
- Enabled database searches by motifs and assessment of promoter similarity across chromosomes.
Main Results:
- Demonstrated the utility of MAGNETIC using the transcription factor Myc and its regulated genes.
- Identified putative novel targets of Myc.
- Revealed instances of indirect gene regulation by Myc.
- Showcased the ability to find motif abundance across all gene promoters and identify potential protein binding sites.
Conclusions:
- MAGNETIC facilitates the discovery of gene regulatory networks and functional gene connections.
- The server provides valuable insights into gene regulation and function.
- MAGNETIC aids in identifying direct and indirect regulatory relationships, exemplified by Myc's interactions.
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