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Biol."],"published-print":{"date-parts":[[2026,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>A gene is essential if its loss of function results in lethality, reduced fitness, or disease. Essential genes have attracted increasing attention due to their vital functions in biological systems. Many efforts have been made to find essential protein\u2010coding genes. In complex organisms, the majority of the genome does not encode proteins. Noncoding genes play vital roles in many biological processes. Investigating the essentiality of noncoding genes is necessary. We present ELE (estimating long noncoding RNA essentiality), the first computational model for finding essential long noncoding RNA (lncRNA) genes in a tissue\u2010specific context. ELE integrates lncRNA\u2010protein\u2013protein interaction (LPPI) network structure with genomic and epigenomic features to predict essential lncRNA genes. With ELE, we identified tissue\u2010specific essential lncRNA genes in human and mouse. Tissue\u2010specific essential lncRNA genes are more involved in physiological context\u2010dependent cellular functions. Moreover, we found that essential lncRNA genes tend to interact more with essential proteins and essential microRNAs (miRNAs). ELE serves as an effective framework for deciphering lncRNA gene essentialities, offering a set of tissue\u2010dependent candidates for further validation. We have deposited all datasets and codes for reproducing ELE results in a GitHub repository (swt1024\/ELE).<\/jats:p>","DOI":"10.1002\/qub2.70053","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T05:49:13Z","timestamp":1790056153000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["ELE: Estimating tissue\u2010specific long noncoding RNA gene essentiality using graph neural networks"],"prefix":"10.1002","volume":"14","author":[{"given":"Wan\u2010Ting","family":"Shi","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology Tianjin University  Tianjin China"},{"name":"College of Intelligence and Computing Tianjin University  Tianjin China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying\u2010Dong","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Intelligence and Computing Tianjin University  Tianjin 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