{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,8]],"date-time":"2026-06-08T17:20:57Z","timestamp":1780939257889,"version":"3.54.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2021,2,24]],"date-time":"2021-02-24T00:00:00Z","timestamp":1614124800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U01AI082110"],"award-info":[{"award-number":["U01AI082110"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>We previously described the construction and characterization of fixed reusable blood transcriptional module repertoires. More recently we released a third iteration (\u2018BloodGen3\u2019 module repertoire) that comprises 382 functionally annotated modules and encompasses 14\u00a0168 transcripts. Custom bioinformatic tools are needed to support downstream analysis, visualization and interpretation relying on such fixed module repertoires.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed and describe here an R package, BloodGen3Module. The functions of our package permit group comparison analyses to be performed at the module-level, and to display the results as annotated fingerprint grid plots. A parallel workflow for computing module repertoire changes for individual samples rather than groups of samples is also available; these results are displayed as fingerprint heatmaps. An illustrative case is used to demonstrate the steps involved in generating blood transcriptome repertoire fingerprints of septic patients. Taken together, this resource could facilitate the analysis and interpretation of changes in blood transcript abundance observed across a wide range of pathological and physiological states.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The BloodGen3Module package and documentation are freely available from Github: https:\/\/github.com\/Drinchai\/BloodGen3Module.<\/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\/btab121","type":"journal-article","created":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T15:42:10Z","timestamp":1614094930000},"page":"2382-2389","source":"Crossref","is-referenced-by-count":36,"title":["BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R"],"prefix":"10.1093","volume":"37","author":[{"given":"Darawan","family":"Rinchai","sequence":"first","affiliation":[{"name":"Research branch, Sidra Medicine , Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"Roelands","sequence":"additional","affiliation":[{"name":"Research branch, Sidra Medicine , Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mohammed","family":"Toufiq","sequence":"additional","affiliation":[{"name":"Research branch, Sidra Medicine , Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7649-5092","authenticated-orcid":false,"given":"Wouter","family":"Hendrickx","sequence":"additional","affiliation":[{"name":"Research branch, Sidra Medicine , Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew C","family":"Altman","sequence":"additional","affiliation":[{"name":"Division of Allergy and Infectious Diseases, University of Washington , Seattle, WA, 98195, USA"},{"name":"Systems Immunology, Benaroya Research Institute , Seattle, WA, 98101, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Davide","family":"Bedognetti","sequence":"additional","affiliation":[{"name":"Research branch, Sidra Medicine , Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6131-7242","authenticated-orcid":false,"given":"Damien","family":"Chaussabel","sequence":"additional","affiliation":[{"name":"Research branch, Sidra Medicine , Doha, Qatar"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,2,24]]},"reference":[{"key":"2023051609143613000_btab121-B1","doi-asserted-by":"crossref","first-page":"1134","DOI":"10.1038\/ni.3028","article-title":"A narrow repertoire of transcriptional modules responsive to pyogenic bacteria is impaired in patients carrying loss-of-function mutations in MYD88 or IRAK4","volume":"15","author":"Alsina","year":"2014","journal-title":"Nat. Immunol"},{"key":"2023051609143613000_btab121-B2","first-page":"587295","volume-title":"A Transcriptome Fingerprinting Assay for Clinical Immune Monitoring","author":"Altman","year":"2019"},{"key":"2023051609143613000_btab121-B3","first-page":"525709","volume-title":"Development and Characterization of a Fixed Repertoire of Blood Transcriptome Modules Based on Co-expression Patterns Across Immunological States","author":"Altman","year":"2020"},{"key":"2023051609143613000_btab121-B4","doi-asserted-by":"crossref","first-page":"e5446","DOI":"10.1371\/journal.pone.0005446","article-title":"Enhanced monocyte response and decreased central memory T cells in children with invasive Staphylococcus aureus infections","volume":"4","author":"Ardura","year":"2009","journal-title":"PLoS One"},{"key":"2023051609143613000_btab121-B5","doi-asserted-by":"crossref","first-page":"e34390","DOI":"10.1371\/journal.pone.0034390","article-title":"Host immune transcriptional profiles reflect the variability in clinical disease manifestations in patients with Staphylococcus aureus infections","volume":"7","author":"Banchereau","year":"2012","journal-title":"PLoS One"},{"key":"2023051609143613000_btab121-B6","doi-asserted-by":"crossref","first-page":"5283","DOI":"10.1038\/ncomms6283","article-title":"Transcriptional specialization of human dendritic cell subsets in response to microbial vaccines","volume":"5","author":"Banchereau","year":"2014","journal-title":"Nat. Commun"},{"key":"2023051609143613000_btab121-B7","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1038\/nature09247","article-title":"An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis","volume":"466","author":"Berry","year":"2010","journal-title":"Nature"},{"key":"2023051609143613000_btab121-B8","doi-asserted-by":"crossref","first-page":"1204","DOI":"10.1038\/s43018-020-00143-y","article-title":"Flt3 ligand augments immune responses to anti-DEC-205-NY-ESO-1 vaccine through expansion of dendritic cell subsets","volume":"1","author":"Bhardwaj","year":"2020","journal-title":"Nat. Cancer"},{"key":"2023051609143613000_btab121-B9","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1016\/j.smim.2015.03.002","article-title":"Assessment of immune status using blood transcriptomics and potential implications for global health","volume":"27","author":"Chaussabel","year":"2015","journal-title":"Semin. Immunol"},{"key":"2023051609143613000_btab121-B10","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1038\/nri3642","article-title":"Democratizing systems immunology with modular transcriptional repertoire analyses","volume":"14","author":"Chaussabel","year":"2014","journal-title":"Nat. Rev. Immunol"},{"key":"2023051609143613000_btab121-B11","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1016\/j.immuni.2008.05.012","article-title":"A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus","volume":"29","author":"Chaussabel","year":"2008","journal-title":"Immunity"},{"key":"2023051609143613000_btab121-B12","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.it.2019.01.003","article-title":"Neglected cells: immunomodulatory roles of CD71+ erythroid cells","volume":"40","author":"Elahi","year":"2019","journal-title":"Trends Immunol"},{"key":"2023051609143613000_btab121-B13","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1111\/j.1749-6632.2010.05731.x","article-title":"The role of the blood transcriptome in innate inflammation and stroke","volume":"1207","author":"Freedman","year":"2010","journal-title":"Ann. N. Y. Acad. Sci"},{"key":"2023051609143613000_btab121-B14","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1016\/j.neulet.2011.03.019","article-title":"Use of peripheral blood transcriptome biomarkers for epilepsy prediction","volume":"497","author":"Karsten","year":"2011","journal-title":"Neurosci. Lett"},{"key":"2023051609143613000_btab121-B15","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1186\/1471-2105-9-559","article-title":"WGCNA: an R package for weighted correlation network analysis","volume":"9","author":"Langfelder","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"2023051609143613000_btab121-B16","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/ni.2789","article-title":"Molecular signatures of antibody responses derived from a systems biology study of five human vaccines","volume":"15","author":"Li","year":"2014","journal-title":"Nat. Immunol"},{"key":"2023051609143613000_btab121-B17","doi-asserted-by":"crossref","first-page":"e1001549","DOI":"10.1371\/journal.pmed.1001549","article-title":"Whole blood gene expression profiles to assess pathogenesis and disease severity in infants with respiratory syncytial virus infection","volume":"10","author":"Mejias","year":"2013","journal-title":"PLoS Med"},{"key":"2023051609143613000_btab121-B18","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1097\/QCO.0000000000000065","article-title":"Detecting specific infections in children through host responses: A paradigm shift","volume":"27","author":"Mejias","year":"2014","journal-title":"Curr. Opin. Infect. Dis"},{"key":"2023051609143613000_btab121-B19","doi-asserted-by":"crossref","first-page":"20140138","DOI":"10.1098\/rstb.2014.0146","article-title":"Vaccinology in the era of high-throughput biology","volume":"370","author":"Nakaya","year":"2015","journal-title":"Philos. Trans. R. Soc. Lond. Ser. B Biol. Sci"},{"key":"2023051609143613000_btab121-B20","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1016\/j.cell.2011.01.004","article-title":"Densely interconnected transcriptional circuits control cell states in human hematopoiesis","volume":"144","author":"Novershtern","year":"2011","journal-title":"Cell"},{"key":"2023051609143613000_btab121-B21","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1016\/j.immuni.2012.12.008","article-title":"Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines","volume":"38","author":"Obermoser","year":"2013","journal-title":"Immunity"},{"key":"2023051609143613000_btab121-B6865352","doi-asserted-by":"crossref","first-page":"R127","DOI":"10.1186\/gb-2009-10-11-r127","article-title":"Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis","volume":"10","author":"Pankla","year":"2009","journal-title":"Genome Biology"},{"key":"2023051609143613000_btab121-B22","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1111\/j.1600-065X.2008.00643.x","article-title":"How the study of children with rheumatic diseases identified interferon-alpha and interleukin-1 as novel therapeutic targets","volume":"223","author":"Pascual","year":"2008","journal-title":"Immunol. Rev"},{"key":"2023051609143613000_btab121-B23","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1146\/annurev-immunol-030409-101221","article-title":"A genomic approach to human autoimmune diseases","volume":"28","author":"Pascual","year":"2010","journal-title":"Annu. Rev. Immunol"},{"key":"2023051609143613000_btab121-B24","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1136\/ard.2010.134254","article-title":"A multicentre, randomised, double-blind, placebo-controlled trial with the interleukin-1 receptor antagonist anakinra in patients with systemic-onset juvenile idiopathic arthritis (ANAJIS trial)","volume":"70","author":"Quartier","year":"2011","journal-title":"Ann. Rheumatic Dis"},{"key":"2023051609143613000_btab121-B25","doi-asserted-by":"crossref","first-page":"587946","DOI":"10.3389\/fimmu.2020.587946","article-title":"A neutrophil-driven inflammatory signature characterizes the blood transcriptome fingerprint of psoriasis","volume":"11","author":"Rawat","year":"2020","journal-title":"Front. Immunol"},{"key":"2023051609143613000_btab121-B26","doi-asserted-by":"crossref","first-page":"919","DOI":"10.12688\/f1000research.7093.2","article-title":"Blood interferon signatures putatively link lack of protection conferred by the RTS,S recombinant malaria vaccine to an antigen-specific IgE response","volume":"4","author":"Rinchai","year":"2017","journal-title":"F1000Research"},{"key":"2023051609143613000_btab121-B27","doi-asserted-by":"crossref","DOI":"10.1002\/ctm2.244","article-title":"Definition of erythroid cell-positive blood transcriptome phenotypes associated with severe respiratory syncytial virus infection","volume":"10","author":"Rinchai","year":"2020","journal-title":"Clin. Transl. Med"},{"key":"2023051609143613000_btab121-B28","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1186\/s12967-020-02456-z","article-title":"A modular framework for the development of targeted Covid-19 blood transcript profiling panels","volume":"18","author":"Rinchai","year":"2020","journal-title":"J. Transl. Med"},{"key":"2023051609143613000_btab121-B29","doi-asserted-by":"crossref","first-page":"2887","DOI":"10.1038\/s41467-019-10601-6","article-title":"Transcriptional profiling unveils type I and II interferon networks in blood and tissues across diseases","volume":"10","author":"Singhania","year":"2019","journal-title":"Nat. Commun"},{"key":"2023051609143613000_btab121-B30","doi-asserted-by":"crossref","first-page":"e1002480","DOI":"10.1371\/journal.ppat.1002480","article-title":"Systems biology approaches reveal a specific interferon-inducible signature in HTLV-1 associated myelopathy","volume":"8","author":"Tattermusch","year":"2012","journal-title":"PLoS Pathog"},{"key":"2023051609143613000_btab121-B31","first-page":"575","article-title":"Gene co-expression analysis for functional classification and gene\u2013disease predictions","volume":"19","author":"van Dam","year":"2017","journal-title":"Brief. Bioinf"},{"key":"2023051609143613000_btab121-B32","first-page":"1381","article-title":"URL decay in MEDLINE\u2013a 4-year follow-up study","volume":"24","author":"Wren","year":"2008","journal-title":"Bioinformatics (Oxford, England)"},{"key":"2023051609143613000_btab121-B33","doi-asserted-by":"crossref","first-page":"3627","DOI":"10.1093\/nar\/gkx182","article-title":"Use it or lose it: citations predict the continued online availability of published bioinformatics resources","volume":"45","author":"Wren","year":"2017","journal-title":"Nucleic Acids Res"},{"key":"2023051609143613000_btab121-B34","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1186\/s12859-018-2338-4","article-title":"Data-driven human transcriptomic modules determined by independent component analysis","volume":"19","author":"Zhou","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2023051609143613000_btab121-B35","doi-asserted-by":"crossref","first-page":"5146","DOI":"10.1093\/bioinformatics\/btz447","article-title":"Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms","volume":"35","author":"Zyla","year":"2019","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab121\/36524031\/btab121.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/16\/2382\/50339616\/btab121.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/16\/2382\/50339616\/btab121.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T05:18:01Z","timestamp":1684214281000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/16\/2382\/6149124"}},"subtitle":[],"editor":[{"given":"Pier Luigi","family":"Martelli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,2,24]]},"references-count":36,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2021,8,25]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab121","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.07.16.205963","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2021,8,15]]},"published":{"date-parts":[[2021,2,24]]}}}