Document Type
Article
Publication Date
11-19-2024
Original Citation
Taub L,
Hampton T,
Sarkar S,
Doing G,
Neff S,
Finger C,
Ferreira Fukutani K,
Stanton B.
E.PathDash, pathway activation analysis of publicly available pathogen gene expression data. mSystems. 2024;9(11):e0103024
Keywords
JGM, Software, Humans, Gene Expression Profiling, Databases, Genetic, Computational Biology
JAX Source
mSystems. 2024;9(11):e0103024
ISSN
2379-5077
PMID
39422483
DOI
https://doi.org/10.1128/msystems.01030-24
Abstract
UNLABELLED: E.PathDash facilitates re-analysis of gene expression data from pathogens clinically relevant to chronic respiratory diseases, including a total of 48 studies, 548 samples, and 404 unique treatment comparisons. The application enables users to assess broad biological stress responses at the KEGG pathway or gene ontology level and also provides data for individual genes. E.PathDash reduces the time required to gain access to data from multiple hours per data set to seconds. Users can download high-quality images such as volcano plots and boxplots, differential gene expression results, and raw count data, making it fully interoperable with other tools. Importantly, users can rapidly toggle between experimental comparisons and different studies of the same phenomenon, enabling them to judge the extent to which observed responses are reproducible. As a proof of principle, we invited two cystic fibrosis scientists to use the application to explore scientific questions relevant to their specific research areas. Reassuringly, pathway activation analysis recapitulated results reported in original publications, but it also yielded new insights into pathogen responses to changes in their environments, validating the utility of the application. All software and data are freely accessible, and the application is available at scangeo.dartmouth.edu/EPathDash.
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 International License.