Imperfect gold standard gene sets yield inaccurate evaluation of causal gene identification methods

Autor:	Lijia Wang, Xiaoquan Wen, Jean Morrison
Jazyk:	angličtina
Rok vydání:	2024
Předmět:	Biology (General) QH301-705.5
Zdroj:	Communications Biology, Vol 7, Iss 1, Pp 1-5 (2024)
Druh dokumentu:	article
ISSN:	2399-3642
DOI:	10.1038/s42003-024-06482-1
Popis:	Abstract Causal gene discovery methods are often evaluated using reference sets of causal genes, which are treated as gold standards (GS) for the purposes of evaluation. However, evaluation methods typically treat genes not in the GS positive set as known negatives rather than unknowns. This leads to inaccurate estimates of sensitivity, specificity, and AUC. Labeling biases in GS gene sets can also lead to inaccurate ordering of alternative causal gene discovery methods. We argue that the evaluation of causal gene discovery methods should rely on statistical techniques like those used for variant discovery rather than on comparison with GS gene sets.
Databáze:	Directory of Open Access Journals
Externí odkaz:	https://doaj.org/article/14932880330945c4993e0d81553678a6 Zobrazit plný text záznamu View record in DOAJ Plný text ve formátu PDF Plný text ve formátu HTML
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