ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data

Helen O Masson; David Borland; Jason Reilly; Adrian Telleria; Shalki Shrivastava; Matt Watson; Luthfi Bustillos; Zerong Li; Laura Capps; Benjamin P Kellman; Zachary A King; Anne Richelle; Nathan E Lewis; Kimberly Robasky

doi:10.1016/j.xpro.2023.102069

ImmCellFie: A user-friendly web-based platform to infer metabolic function from omics data

STAR Protoc. 2023 Mar 17;4(1):102069. doi: 10.1016/j.xpro.2023.102069. Epub 2023 Jan 25.

Authors

Affiliations

¹ Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA.
² Renaissance Computing Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA.
³ Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA.
⁴ Bioinformatics and Systems Biology Program, UC San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA.
⁵ Department of Bioengineering, UC San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, UC San Diego, La Jolla, CA 92093, USA. Electronic address: nlewisres@ucsd.edu.
⁶ Renaissance Computing Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel H0069ll, NC 27514, USA; School of Information and Library Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Carolina Health and Informatics Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address: kimberly.robasky@gmail.com.

Abstract

Understanding cellular metabolism is important across biotechnology and biomedical research and has critical implications in a broad range of normal and pathological conditions. Here, we introduce the user-friendly web-based platform ImmCellFie, which allows the comprehensive analysis of metabolic functions inferred from transcriptomic or proteomic data. We explain how to set up a run using publicly available omics data and how to visualize the results. The ImmCellFie algorithm pushes beyond conventional statistical enrichment and incorporates complex biological mechanisms to quantify cell activity. For complete details on the use and execution of this protocol, please refer to Richelle et al. (2021).¹.

Keywords: Bioinformatics; Genomics; Metabolism; Systems Biology.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Computational Biology* / methods
Internet
Proteomics* / methods

Abstract

Publication types

MeSH terms

Grants and funding