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

BMC Bioinformatics. 2019 Jul 18;20(1):399. doi: 10.1186/s12859-019-2971-6.

Abstract

Background: High-throughput experiments can bring to light associations between genes, proteins and/or metabolites, many of which will be explainable by existing knowledge. Our aim is to speed elucidation of such explanations and, in some cases, find explanations that scientists might otherwise overlook.

Results: We describe the MultiOmics Explainer, a new tool within the Pathway Tools software suite that leverages what is known about an organism's metabolic and regulatory network to suggest explanations for the results of omics experiments. Querying a database such as EcoCyc, the MultiOmics Explainer searches the organism's network of metabolic reactions, transporters, cofactors, enzyme substrate-level activation and inhibition relationships, and transcriptional and translational regulation relationships to identify paths of influence among input genes, proteins and metabolites. Results are presented in a combined metabolic and regulatory diagram. We present several examples of explanations generated for associations found in the Escherichia coli literature.

Conclusions: The MultiOmics Explainer is a valuable tool that helps researchers understand and interpret the results of their omics experiments in the context of what is known about an organism's metabolic and regulatory network. It showcases the rich set of computational inferences that can be drawn from a database such as EcoCyc that encodes a diverse range of biological interactions.

Keywords: Multiomics analysis; Network analysis; Pathfinding; Pathway visualization; Pathway/genome database.

MeSH terms

  • Databases, Factual
  • Databases, Genetic
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Gene Expression Profiling*
  • Genome
  • Metabolic Networks and Pathways
  • Metabolomics*
  • Proteomics*
  • Software*