{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:42Z","timestamp":1772138082161,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2017,2,8]],"date-time":"2017-02-08T00:00:00Z","timestamp":1486512000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100015503","name":"Lieber Institute for Brain Development","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100015503","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Cleveland Foundation and Johns Hopkins University Discovery"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,6,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Non-negative Matrix Factorization (NMF) algorithms associate gene expression with biological processes (e.g. time-course dynamics or disease subtypes). Compared with univariate associations, the relative weights of NMF solutions can obscure biomarkers. Therefore, we developed a novel patternMarkers statistic to extract genes for biological validation and enhanced visualization of NMF results. Finding novel and unbiased gene markers with patternMarkers requires whole-genome data. Therefore, we also developed Genome-Wide CoGAPS Analysis in Parallel Sets (GWCoGAPS), the first robust whole genome Bayesian NMF using the sparse, MCMC algorithm, CoGAPS. Additionally, a manual version of the GWCoGAPS algorithm contains analytic and visualization tools including patternMatcher, a Shiny web application. The decomposition in the manual pipeline can be replaced with any NMF algorithm, for further generalization of the software. Using these tools, we find granular brain-region and cell-type specific signatures with corresponding biomarkers in GTEx data, illustrating GWCoGAPS and patternMarkers ascertainment of data-driven biomarkers from whole-genome data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>PatternMarkers &amp; GWCoGAPS are in the CoGAPS Bioconductor package (3.5) under the GPL license.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx058","type":"journal-article","created":{"date-parts":[[2017,1,30]],"date-time":"2017-01-30T08:28:22Z","timestamp":1485764902000},"page":"1892-1894","source":"Crossref","is-referenced-by-count":56,"title":["PatternMarkers &amp; GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF"],"prefix":"10.1093","volume":"33","author":[{"given":"Genevieve L","family":"Stein-O\u2019Brien","sequence":"first","affiliation":[{"name":"McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA"},{"name":"Lieber Institute for Brain Development, Baltimore, MD, USA"}]},{"given":"Jacob L","family":"Carey","sequence":"additional","affiliation":[{"name":"Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA"}]},{"given":"Wai Shing","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA"}]},{"given":"Michael","family":"Considine","sequence":"additional","affiliation":[{"name":"Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA"}]},{"given":"Alexander V","family":"Favorov","sequence":"additional","affiliation":[{"name":"Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA"},{"name":"Vavilov Institute of General Genetics, Moscow, Russia"},{"name":"Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia"}]},{"given":"Emily","family":"Flam","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA"}]},{"given":"Theresa","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA"}]},{"given":"Sijia","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA"}]},{"given":"Luigi","family":"Marchionni","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA"}]},{"given":"Thomas","family":"Sherman","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA"}]},{"given":"Shawn","family":"Sivy","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA"}]},{"given":"Daria A","family":"Gaykalova","sequence":"additional","affiliation":[{"name":"Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA"}]},{"given":"Ronald D","family":"McKay","sequence":"additional","affiliation":[{"name":"Lieber Institute for Brain Development, Baltimore, MD, USA"}]},{"given":"Michael F","family":"Ochs","sequence":"additional","affiliation":[{"name":"Department of Mathematics and Statistics, The College of New Jersey, Ewing Township, NJ, USA"}]},{"given":"Carlo","family":"Colantuoni","sequence":"additional","affiliation":[{"name":"Department of Neurology and Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA"},{"name":"Institute for Genome Sciences, University of Maryland School of Medicine"}]},{"given":"Elana J","family":"Fertig","sequence":"additional","affiliation":[{"name":"Department of Oncology and Division of Biostatistics and Bioinformatics, Johns Hopkins School of Medicine, Baltimore, MD, USA"}]}],"member":"286","published-online":{"date-parts":[[2017,2,8]]},"reference":[{"key":"2023020205473917700_btx058-B1","doi-asserted-by":"crossref","first-page":"4164","DOI":"10.1073\/pnas.0308531101","article-title":"Metagenes and molecular pattern discovery using matrix factorization","volume":"101","author":"Brunet","year":"2004","journal-title":"Proc. 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