IMPRINTS.CETSA and IMPRINTS.CETSA.app: an R package and a Shiny application for the analysis and interpretation of IMPRINTS-CETSA data

Abstract IMPRINTS-CETSA (Integrated Modulation of Protein Interaction States—Cellular Thermal Shift Assay) provides a highly resolved means to systematically study the interactions of proteins with other cellular components, including metabolites, nucleic acids and other proteins, at the proteome le...

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Bibliographic Details
Published in:Briefings in bioinformatics 2024-03, Vol.25 (3)
Main Authors: Gerault, Marc-Antoine, Granjeaud, Samuel, Camoin, Luc, Nordlund, Pär, Dai, Lingyun
Format: Article
Language:English
Subjects:
Algorithms
Data analysis
Data processing
Medicin och hälsovetenskap
Metabolites
Nucleic acids
Problem Solving Protocol
Proteins
Proteomes
Robustness (mathematics)
Thermal stability
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Summary:Abstract IMPRINTS-CETSA (Integrated Modulation of Protein Interaction States—Cellular Thermal Shift Assay) provides a highly resolved means to systematically study the interactions of proteins with other cellular components, including metabolites, nucleic acids and other proteins, at the proteome level, but no freely available and user-friendly data analysis software has been reported. Here, we report IMPRINTS.CETSA, an R package that provides the basic data processing framework for robust analysis of the IMPRINTS-CETSA data format, from preprocessing and normalization to visualization. We also report an accompanying R package, IMPRINTS.CETSA.app, which offers a user-friendly Shiny interface for analysis and interpretation of IMPRINTS-CETSA results, with seamless features such as functional enrichment and mapping to other databases at a single site. For the hit generation part, the diverse behaviors of protein modulations have been typically segregated with a two-measure scoring method, i.e. the abundance and thermal stability changes. We present a new algorithm to classify modulated proteins in IMPRINTS-CETSA experiments by a robust single-measure scoring. In this way, both the numerical changes and the statistical significances of the IMPRINTS information can be visualized on a single plot. The IMPRINTS.CETSA and IMPRINTS.CETSA.app R packages are freely available on GitHub at https://github.com/nkdailingyun/IMPRINTS.CETSA and https://github.com/mgerault/IMPRINTS.CETSA.app, respectively. IMPRINTS.CETSA.app is also available as an executable program at https://zenodo.org/records/10636134.
ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbae128