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The common strategy of computing consensus orthologs introduces additional arbitrariness, emphasizing the need to examine the causes of such inconsistencies and identify proteins susceptible to prediction errors.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We introduce the Signal Jaccard Index (SJI), a novel metric rooted in unsupervised genome context clustering, designed to assess protein similarity. Leveraging SJI, we construct a protein network and reveal that peripheral proteins within the network are the primary contributors to inconsistencies in orthology predictions. Furthermore, we show that a protein's degree centrality in the network serves as a strong predictor of its reliability in consensus sets.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>We present an objective, unsupervised SJI-based network encompassing all proteins, in which its topological features elucidate ortholog prediction inconsistencies. The degree centrality (DC) effectively identifies error-prone orthology assignments without relying on arbitrary parameters. Notably, DC is stable, unaffected by species selection, and well-suited for ortholog benchmarking. This approach transcends the limitations of universal thresholds, offering a robust and quantitative framework to explore protein evolution and functional relationships.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-024-06023-x","type":"journal-article","created":{"date-parts":[[2025,1,7]],"date-time":"2025-01-07T08:25:22Z","timestamp":1736238322000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["A metric and its derived protein network for evaluation of ortholog database inconsistency"],"prefix":"10.1186","volume":"26","author":[{"given":"Weijie","family":"Yang","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jingsi","family":"Ji","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gang","family":"Fang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,1,7]]},"reference":[{"key":"6023_CR1","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1146\/annurev.genet.39.073003.114725","volume":"39","author":"EV Koonin","year":"2005","unstructured":"Koonin EV. 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