Immune Cellular Functions Inference (ImmCellFie)

ImmCellFie is a portal for inferring cellular function given gene expression samples and their phenotypical data, based on the CellFie (Cellular Functions Inference) approach. CellFie combines a detailed systems biology input/output approach with the simplicity of enrichment analysis. The CellFie method involves generating a set of curated model-derived “metabolic tasks,” which are precomputed sets of genes that together consume a metabolite at the start of a pathway and produce a final metabolic product of interest. Using CellFie, one can overlay transcriptomic or proteomic data onto these precomputed gene modules to predict pathway usage for each metabolic task, thus providing properties-relevant interpretation of how changes in complex omics experiments modify cell or tissue metabolic function.

The ImmCellFie Portal makes CellFie accessible to the broader immunology community and beyond by providing an easy-to-use and easy-to-extend webportal housing the CellFie toolbox. ImmCellFie integrates ImmPort data with other data sources enabling users to process and compare data using the CellFie algorithm. ImmCellFie includes interactive visualization tools including heatmaps, treemaps, and Escher pathway visualizations to facilitate exploration and interpretability of CellFie results.

Kimberly Robasky was co-PI with UCSD’s Nate Lewis; RENCI designed, implemented, and deploying advanced visualizations and sustainable infrastructure for running systems biology and other tools on a plugin architecture that serves as a gateway for running bioinformatics tools on geographically dispersed data sources.

• University of California San Diego

• National Institute of Allergy and Infectious Diseases (NIAID)