{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T08:27:34Z","timestamp":1771662454670,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2019,1,8]],"date-time":"2019-01-08T00:00:00Z","timestamp":1546905600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100003593","name":"CNPq","doi-asserted-by":"publisher","award":["444856\/2014\u20135"],"award-info":[{"award-number":["444856\/2014\u20135"]}],"id":[{"id":"10.13039\/501100003593","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002322","name":"CAPES","doi-asserted-by":"publisher","award":["3381\/2013"],"award-info":[{"award-number":["3381\/2013"]}],"id":[{"id":"10.13039\/501100002322","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,8,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Several freely available tools perform analysis using algorithms developed to identify significant variation of gene expression individually. The transcriptogramer R package uses protein\u2013protein interaction to perform differential expression of functionally associated genes. The software assesses expression profile of entire genetic systems and reveals which biological systems are significantly altered in case-control designed transcriptome experiments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>R\/Bioconductor transcriptogramer package projects expression values on an ordered gene list to perform topological analysis, differential expression and gene ontology enrichment analysis, independently of data platform or operating system.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>http:\/\/bioconductor.org\/packages\/transcriptogramer.<\/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\/btz007","type":"journal-article","created":{"date-parts":[[2019,1,5]],"date-time":"2019-01-05T04:50:49Z","timestamp":1546663849000},"page":"2875-2876","source":"Crossref","is-referenced-by-count":10,"title":["Transcriptogramer: an R\/Bioconductor package for transcriptional analysis based on protein\u2013protein interaction"],"prefix":"10.1093","volume":"35","author":[{"given":"Diego A A","family":"Morais","sequence":"first","affiliation":[{"name":"Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, RN, Brazil"}]},{"given":"Rita M C","family":"Almeida","sequence":"additional","affiliation":[{"name":"Institute of Physics and National Institute of Science and Technology: Complex Systems, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil"}]},{"given":"Rodrigo J S","family":"Dalmolin","sequence":"additional","affiliation":[{"name":"Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, RN, Brazil"},{"name":"Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil"}]}],"member":"286","published-online":{"date-parts":[[2019,1,8]]},"reference":[{"key":"2023062708583241300_btz007-B1","first-page":"1600","article-title":"Improved scoring of functional groups from gene expression data by decorrelating GO graph structure","volume-title":"Bioinformatics","author":"Alexa","year":"2006"},{"key":"2023062708583241300_btz007-B2","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1038\/nprot.2013.099","article-title":"Count-based differential expression analysis of RNA sequencing data using R and Bioconductor","volume":"8","author":"Anders","year":"2013","journal-title":"Nat. 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