ArticleBMC infectious diseases2021
Comparing tuberculosis gene signatures in malnourished individuals using the TBSignatureProfiler.
Article in BMC infectious diseases, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 23 citations in OpenAlex.
- Adjunctive ibuprofen in pre-extensively drug-resistant and extensively drug-resistant tuberculosis: a phase IIA open-label pilot clinical trial.Nature communications · 2026Trial
- Monocyte-Amplified Transcriptional Signatures of Human Diseases.bioRxiv : the preprint server for biology · 2026Article
- A Deep Representation Learning Method for Quantitative Immune Defense Function Evaluation and Its Clinical Applications.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Nasal Gene Expression in ART-Naive Adults with HIV and Pulmonary Tuberculosis in Uganda.medRxiv : the preprint server for health sciences · 2026Article
- Article
- Analysis of the cross-study replicability of tuberculosis gene signatures using 49 curated human transcriptomic datasets.Tuberculosis (Edinburgh, Scotland) · 2025Article
- Prominence of Mycobacterium tuberculosis biomarkers among sputum culture-negative clinic attendees, independent of Ultra status.Journal of infection and public health · 2025Article
- Cross-species transcriptomics translation reveals a role for the unfolded protein response in Mycobacterium tuberculosis infection.NPJ systems biology and applications · 2025Article
- Comparison of gene set scoring methods for reproducible evaluation of tuberculosis gene signatures.BMC infectious diseases · 2024Article
- Article
- A protein signature associated with active tuberculosis identified by plasma profiling and network-based analysis.iScience · 2022Article
- Development and Validation of a Parsimonious Tuberculosis Gene Signature Using the digital NanoString nCounter Platform.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2022Article
- Comprehensive lipid and lipid-related gene investigations of host immune responses to characterize metabolism-centric biomarkers for pulmonary tuberculosis.Scientific reports · 2022Article
- Transcriptomics for child and adolescent tuberculosis.Immunological reviews · 2022Review
- Malnutrition leads to increased inflammation and expression of tuberculosis risk signatures in recently exposed household contacts of pulmonary tuberculosis.Frontiers in immunology · 2022Article
Corrections and comments
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Authors and funding
17 authors at 4 institutions in 2 countries.
Funding
Abstract
backgroundGene expression signatures have been used as biomarkers of tuberculosis (TB) risk and outcomes. Platforms are needed to simplify access to these signatures and determine their validity in the setting of comorbidities. We developed a computational profiling platform of TB signature gene sets and characterized the diagnostic ability of existing signature gene sets to differentiate active TB from LTBI in the setting of malnutrition.
methodsWe curated 45 existing TB-related signature gene sets and developed our TBSignatureProfiler software toolkit that estimates gene set activity using multiple enrichment methods and allows visualization of single- and multi-pathway results. The TBSignatureProfiler software is available through Bioconductor and on GitHub. For evaluation in malnutrition, we used whole blood gene expression profiling from 23 severely malnourished Indian individuals with TB and 15 severely malnourished household contacts with latent TB infection (LTBI). Severe malnutrition was defined as body mass index (BMI) < 16 kg/m2 in adults and based on weight-for-height Z scores in children < 18 years. Gene expression was measured using RNA-sequencing.
resultsThe comparison and visualization functions from the TBSignatureProfiler showed that TB gene sets performed well in malnourished individuals; 40 gene sets had statistically significant discriminative power for differentiating TB from LTBI, with area under the curve ranging from 0.662-0.989. Three gene sets were not significantly predictive.
conclusionOur TBSignatureProfiler is a highly effective and user-friendly platform for applying and comparing published TB signature gene sets. Using this platform, we found that existing gene sets for TB function effectively in the setting of malnutrition, although differences in gene set applicability exist. RNA-sequencing gene sets should consider comorbidities and potential effects on diagnostic performance.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.