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Advances in functional genomics, particularly gene expression analysis, have made possible genome-wide interrogation of a pathogen to decipher pathogenicity-associated genes. Standard protocols assess differential expression of genes during pathogenesis; however, often a conservative approach is taken, which requires expression fold change above an arbitrarily defined threshold and a statistical significance test to infer a gene as differentially expressing. This renders a high-confidence set of differentially expressed genes in pathogenesis, however, at the cost of numerous false negatives. To circumvent this problem and comprehensively catalog pathogenicity-associated genes, we have developed a novel pipeline that uses standard protocol in combination with gene co-expression network of a pathogen constructed using publicly available RNA-Seq data sets. We assessed the efficacy of this pipeline on\n            <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n            PAO1, a model bacterial pathogen, highlighting the power of our network-based approach in discovering novel genes or pathways associated with the pathogenesis, or antibiotic resistance of this strain. Complementing standard protocol with a gene network-based method thus elevated the ability to identify pathogenicity-associated genes in\n            <jats:italic>P<\/jats:italic>\n            .\n            <jats:italic>aeruginosa<\/jats:italic>\n            PAO1.\n          <\/jats:p>\n          <jats:sec>\n            <jats:title>IMPORTANCE<\/jats:title>\n            <jats:p>\n              We present here a new systems-level approach to decipher genetic factors and biological pathways associated with virulence and\/or antibiotic treatment of bacterial pathogens. The power of this approach was demonstrated by application to a well-studied pathogen\n              <jats:italic>Pseudomonas aeruginosa<\/jats:italic>\n              PAO1. Our gene co-expression network-based approach unraveled known and unknown genes and their networks associated with pathogenicity in\n              <jats:italic>P. aeruginosa<\/jats:italic>\n              PAO1. The systems-level investigation of\n              <jats:italic>P. aeruginosa<\/jats:italic>\n              PAO1 helped identify putative pathogenicity and resistance-associated genetic factors that could not otherwise be detected by conventional approaches of differential gene expression analysis. The network-based analysis uncovered modules that harbor genes not previously reported by several original studies on\n              <jats:italic>P. aeruginosa<\/jats:italic>\n              virulence and resistance. These could potentially act as molecular determinants of\n              <jats:italic>P. aeruginosa<\/jats:italic>\n              PAO1 pathogenicity and responses to antibiotics.\n            <\/jats:p>\n          <\/jats:sec>","DOI":"10.1128\/msystems.00473-23","type":"journal-article","created":{"date-parts":[[2023,11,3]],"date-time":"2023-11-03T13:01:18Z","timestamp":1699016478000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":4,"title":["A gene network-driven approach to infer novel pathogenicity-associated genes: application to\n            <i>Pseudomonas aeruginosa<\/i>\n            PAO1"],"prefix":"10.1128","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6328-0132","authenticated-orcid":false,"given":"Ronika","family":"De","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of North Texas, Denton, Texas, USA"},{"name":"BioDiscovery Institute, University of North Texas, Denton, Texas, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4933-9983","authenticated-orcid":true,"given":"Marvin","family":"Whiteley","sequence":"additional","affiliation":[{"name":"Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA"},{"name":"Emory-Children\u2019s Cystic Fibrosis Center, Atlanta, Georgia, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6874-6146","authenticated-orcid":false,"given":"Rajeev K.","family":"Azad","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of North Texas, Denton, Texas, USA"},{"name":"BioDiscovery Institute, University of North Texas, Denton, Texas, USA"},{"name":"Department of Mathematics, University of North Texas, Denton, Texas, 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