SalmonAct deciphers transcription factor regulatory activity in Salmonella transcriptomics
File(s)
Published version
Author(s)
Olbei, Marton
Bohar, Balazs
Kingsley, Robert A
Korcsmaros, Tamas
Type
Journal Article
Abstract
Foodborne Salmonella enterica infection remains a major public healththreat due to its prevalence in food, ease of transmission, and increasing antibiotic resistance. Consequently, understanding the molecular mechanisms underlyingSalmonella pathogenesis is crucial for guiding novel diagnostic, preventative, andtherapeutic approaches. High-throughput transcriptomic technologies are now oftenemployed in Salmonella research to quantify how gene expression changes in responseto various conditions or mutations. But due to the high dimensionality of this data,resulting from the comparison of the expression of thousands of genes from multiple strains or culture conditions with complex interactions, interpretation remains ademanding task. To address this issue, we present SalmonAct, a comprehensive signedand directed prior knowledge resource for inferring transcription factor activities inSalmonella. This new resource expands the toolkit available for Salmonella functionalanalysis. Built as an extension of the SalmoNet2 database, SalmonAct can be usedto infer the activity of 191 transcription factors in 5,991 regulatory interactions basedon publicly available interaction and regulatory knockout data. SalmonAct enhancesthe interpretation of highly dimensional transcriptomic data by identifying both highlyinfluential and minimally active transcription factors that drive the observed expressionstate. SalmonAct aids in bridging the gap between model and non-model organisms'functional analysis, and together with the SalmoNet2 resource, can be used for furtherdownstream data analyses.
Editor(s)
Gambino, Michela
Date Issued
2026-03-30
Date Acceptance
2026-03-01
Citation
mSystems, 2026, 0 (0)
ISSN
2379-5077
Publisher
American Society for Microbiology
Start Page
e0123925
Journal / Book Title
mSystems
Volume
0
Issue
0
Copyright Statement
© 2026 Olbei et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.
License URL
Identifier
https://www.ncbi.nlm.nih.gov/pubmed/41910312
Subjects
Salmonella
regulatory network
transcription factors
transcriptomics
Publication Status
Published online
Coverage Spatial
United States
Article Number
01239-25
Date Publish Online
2026-03-30