The MultiOmics Explainer: explaining omics results in the context of a pathway/genome database

Area of Science:

• Systems Biology
• Bioinformatics
• Computational Biology

Background:

• High-throughput omics experiments reveal numerous associations between biological molecules.
• Many associations are explainable by existing biological knowledge.
• Elucidating these associations can be time-consuming and may lead to overlooked insights.

Purpose of the Study:

• To develop a computational tool that accelerates the explanation of omics experiment findings.
• To identify biological explanations that might otherwise be missed by researchers.
• To integrate omics data with existing knowledge of metabolic and regulatory networks.

Main Methods:

• The MultiOmics Explainer tool was developed within the Pathway Tools software suite.
• It queries biological databases (e.g., EcoCyc) to access organism-specific metabolic and regulatory network information.
• The tool identifies paths of influence among input genes, proteins, and metabolites using reaction, transporter, cofactor, enzyme, and regulation data.

Main Results:

• The MultiOmics Explainer suggests explanations for omics experiment results by analyzing biological networks.
• It visualizes identified paths of influence in combined metabolic and regulatory diagrams.
• Examples of explanations for Escherichia coli associations are presented.

Conclusions:

• The MultiOmics Explainer is a valuable tool for interpreting omics data within the context of known biological networks.
• It demonstrates the power of computational inferences from comprehensive biological databases like EcoCyc.
• The tool enhances understanding of complex biological interactions revealed by omics studies.