ArticlePeerJ2013
Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures.
Article in PeerJ, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
36 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Blood gene expression risk profiles and interstitial lung abnormalities: COPDGene and ECLIPSE cohort studies.Respiratory research · 2022Pooled it
- Targeting the stringent response alters gene expression and extracellular vesicle RNA inMicrobiology spectrum · 2026Article
- Longitudinal gene expression analysis in COVID-19 sepsis highlights dynamic immune, cellular, and metabolic dysfunction in high severity patients.Scientific reports · 2025Article
- HSAInternational journal of molecular sciences · 2025Article
- Time-course transcriptomics reveals the impact ofFrontiers in microbiology · 2025Article
- Predictive gene expression signature diagnoses neonatal sepsis before clinical presentation.EBioMedicine · 2024Article
- Facilitating pathway and network based analysis of RNA-Seq data with pathlinkR.PLoS computational biology · 2024Article
- Colocalization analysis of 3' UTR alternative polyadenylation quantitative trait loci reveals novel mechanisms underlying associations with lung function.Human molecular genetics · 2024Article
- Blood Gene Expression and Immune Cell Subtypes Associated with Chronic Obstructive Pulmonary Disease Exacerbations.American journal of respiratory and critical care medicine · 2023Article
- Post-COVID symptoms are associated with endotypes reflecting poor inflammatory and hemostatic modulation.Frontiers in immunology · 2023Article
- Facilitating systems-level analyses of all-cause and Covid-mediated sepsis through SeptiSearch, a manually-curated compendium of dysregulated gene sets.Frontiers in immunology · 2023Article
- Article
- Detecting genetic epistasis by differential departure from independence.Molecular genetics and genomics : MGG · 2022Article
- Development of a Blood-based Transcriptional Risk Score for Chronic Obstructive Pulmonary Disease.American journal of respiratory and critical care medicine · 2022Article
- Subcutaneous adipose tissue splice quantitative trait loci reveal differences in isoform usage associated with cardiometabolic traits.American journal of human genetics · 2022Article
- A transcriptomic analysis of the effects of macrophage polarization and endotoxin tolerance on the response to Salmonella.PloS one · 2022Article
- Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria.BMC genomics · 2021Article
- Systems Biology Methods Applied to Blood and Tissue for a Comprehensive Analysis of Immune Response to Hepatitis B Vaccine in Adults.Frontiers in immunology · 2020Observational
- Article
- Whole blood transcriptional responses of very preterm infants during late-onset sepsis.PloS one · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation. Predominant pathway analysis approaches treat pathways as collections of individual genes and consider all pathway members as equally informative. As a result, at times spurious and misleading pathways are inappropriately identified as statistically significant, solely due to components that they share with the more relevant pathways. Results. We introduce the concept of Pathway Gene-Pair Signatures (Pathway-GPS) as pairs of genes that, as a combination, are specific to a single pathway. We devised and implemented a novel approach to pathway analysis, Signature Over-representation Analysis (SIGORA), which focuses on the statistically significant enrichment of Pathway-GPS in a user-specified gene list of interest. In a comparative evaluation of several published datasets, SIGORA outperformed traditional methods by delivering biologically more plausible and relevant results. Availability. An efficient implementation of SIGORA, as an R package with precompiled GPS data for several human and mouse pathway repositories is available for download from http://sigora.googlecode.com/svn/.
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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.