Discovering relationships between nuclear receptor signaling pathways, genes, and tissues in Transcriptomine

Area of Science:

• Molecular Biology
• Genomics
• Bioinformatics

Background:

• Nuclear receptors are key regulators of gene expression.
• Understanding their signaling pathways is crucial for various biological processes.
• Existing tools may lack comprehensive integration of diverse experimental data.

Purpose of the Study:

• To enhance the Transcriptomine web tool for exploring nuclear receptor signaling pathways.
• To improve biocuration, query interface, and data visualization for easier access to biological insights.
• To facilitate the discovery of uncharacterized biology within these pathways.

Main Methods:

• Systematic curation of public expression profiling data sets.
• Classification of experimental manipulations (small molecules, gene targets) into signaling pathways.
• Mapping of tissues and cell lines to physiological systems and organs.
• Integration of data from animal, cell, and clinical models.
• Analysis of transcriptional cross-talk with non-nuclear receptor pathways.

Main Results:

• Transcriptomine now contains ~45 million data points from over 2000 experiments across ~550 curated data sets.
• Enhanced classification enables evaluation of tissue-specific gene regulation by nuclear receptors.
• Data integration validates findings across isolated data sets, revealing roles in normal and pathological processes.
• Identified transcriptional cross-talk between nuclear receptors and other signaling pathways.

Conclusions:

• Transcriptomine serves as a valuable resource for bench biologists to formulate research hypotheses.
• The tool facilitates validation of experimental data and modeling of complex biological relationships.
• Enhanced features promote routine discovery of novel biological insights in nuclear receptor signaling.