{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,20]],"date-time":"2026-09-20T23:36:05Z","timestamp":1789947365923,"version":"4.0.1"},"reference-count":34,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2019,3,28]],"date-time":"2019-03-28T00:00:00Z","timestamp":1553731200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2019,3,28]],"date-time":"2019-03-28T00:00:00Z","timestamp":1553731200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Oral Health"],"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Chronic periodontitis (CP) is a multifactorial inflammatory disease. For the diagnosis of CP, it is necessary to investigate molecular biomarkers and the biological pathway of CP. Although analysis of mRNA expression profiling with microarray is useful to elucidate pathological mechanisms of multifactorial diseases, it is expensive. Therefore, we utilized pooled microarray gene expression data on the basis of data sharing to reduce hybridization costs and compensate for insufficient mRNA sampling. The aim of the present study was to identify molecular biomarker candidates and biological pathways of CP using pooled datasets in the Gene Expression Omnibus (GEO) database.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>Three pooled transcriptomic datasets (GSE10334, GSE16134, and GSE23586) of gingival tissue with CP in the GEO database were analyzed for differentially expressed genes (DEGs) using GEO2R, functional analysis and biological pathways with the Database of Annotation Visualization and Integrated Discovery database, Protein-Protein Interaction (PPI) network and hub gene with the Search Tool for the Retrieval of Interaction Genes database, and biomarker candidates for diagnosis and prognosis and upstream regulators of dominant biomarker candidates with the Ingenuity Pathway Analysis database.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We shared pooled microarray datasets in the GEO database. One hundred and twenty-three common DEGs were found in gingival tissue with CP, including 81 upregulated genes and 42 downregulated genes. Upregulated genes in Gene Ontology were significantly enriched in immune responses, and those in the Kyoto Encyclopedia of Genes and Genomes pathway were significantly enriched in the cytokine-cytokine receptor interaction pathway, cell adhesion molecules, and hematopoietic cell lineage. From the PPI network, the 12 nodes with the highest degree were screened as hub genes. Additionally, six biomarker candidates for CP diagnosis and prognosis were screened.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>We identified several potential biomarkers for CP diagnosis and prognosis (e.g., <jats:italic>CSF3, CXCL12<\/jats:italic>, <jats:italic>IL1B<\/jats:italic>, <jats:italic>MS4A1<\/jats:italic>, <jats:italic>PECAM1<\/jats:italic>, and <jats:italic>TAGLN<\/jats:italic>) and upstream regulators of biomarker candidates for CP diagnosis (<jats:italic>TNF<\/jats:italic> and <jats:italic>TGF2<\/jats:italic>). We also confirmed key genes of CP pathogenesis such as <jats:italic>CD19<\/jats:italic>, <jats:italic>IL8<\/jats:italic>, <jats:italic>CD79A<\/jats:italic>, <jats:italic>FCGR3B<\/jats:italic>, <jats:italic>SELL<\/jats:italic>, <jats:italic>CSF3<\/jats:italic>, <jats:italic>IL1B<\/jats:italic>, <jats:italic>FCGR2B<\/jats:italic>, <jats:italic>CXCL12<\/jats:italic>, <jats:italic>C3<\/jats:italic>, <jats:italic>CD53<\/jats:italic>, and <jats:italic>IL10RA<\/jats:italic>. To our knowledge, this is the first report to reveal associations of <jats:italic>CD53<\/jats:italic>, <jats:italic>CD79A<\/jats:italic>, <jats:italic>MS4A1<\/jats:italic>, <jats:italic>PECAM1<\/jats:italic>, and <jats:italic>TAGLN<\/jats:italic> with CP.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12903-019-0738-0","type":"journal-article","created":{"date-parts":[[2019,3,28]],"date-time":"2019-03-28T07:02:56Z","timestamp":1553756576000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":33,"title":["RETRACTED ARTICLE: Investigation of molecular biomarker candidates for diagnosis and prognosis of chronic periodontitis by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus (GEO)"],"prefix":"10.1186","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6124-8363","authenticated-orcid":false,"given":"Asami","family":"Suzuki","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tetsuro","family":"Horie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yukihiro","family":"Numabe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2019,3,28]]},"reference":[{"key":"738_CR1","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1111\/jcpe.12650","volume":"44","author":"P Bouchard","year":"2017","unstructured":"Bouchard P, Carra MC, Boillot A, Mora F, Rang\u00e9 H. 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Please see the Retraction Notice for more detail:","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"https:\/\/doi.org\/10.1186\/s12903-024-04383-7","URL":"https:\/\/doi.org\/10.1186\/s12903-024-04383-7","order":7,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"52"}}