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Combining data from ENCODE and TCGA datasets, we built a predictive linear model for the regulation of each target gene, assessing the relationships between its expression, promoter methylation, expression of genes in the same or in the other pathways and of putative transcription factors. We proved the reliability and significance of our approach in a similar tumor type (basal-like Breast cancer) and using a different existing algorithm (ARACNe), and we obtained experimental confirmations on potentially interesting results.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The analysis of the proposed models allowed disclosing the relations between a gene and its related biological processes, the interconnections between the different gene sets, and the evaluation of the relevant regulatory elements at single gene level. This led to the identification of already known regulators and\/or gene correlations and to unveil a set of still unknown and potentially interesting biological relationships for their pharmacological and clinical use.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-021-04481-1","type":"journal-article","created":{"date-parts":[[2021,11,27]],"date-time":"2021-11-27T10:02:28Z","timestamp":1638007348000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Predictive modeling of gene expression regulation"],"prefix":"10.1186","volume":"22","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9316-8552","authenticated-orcid":false,"given":"Chiara","family":"Regondi","sequence":"first","affiliation":[]},{"given":"Maddalena","family":"Fratelli","sequence":"additional","affiliation":[]},{"given":"Giovanna","family":"Damia","sequence":"additional","affiliation":[]},{"given":"Federica","family":"Guffanti","sequence":"additional","affiliation":[]},{"given":"Monica","family":"Ganzinelli","sequence":"additional","affiliation":[]},{"given":"Matteo","family":"Matteucci","sequence":"additional","affiliation":[]},{"given":"Marco","family":"Masseroli","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,11,27]]},"reference":[{"issue":"11","key":"4481_CR1","doi-asserted-by":"publisher","first-page":"780","DOI":"10.1007\/s12094-006-0132-7","volume":"8","author":"MD Delgado","year":"2006","unstructured":"Delgado MD, et al. 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