Clover: An unbiased method for prioritizing differentially expressed genes using a data‐driven approach DOI Creative Commons
Gina Miku Oba, Ryuichiro Nakato

Genes to Cells, Journal Year: 2024, Volume and Issue: 29(6), P. 456 - 470

Published: April 11, 2024

Abstract Identifying key genes from a list of differentially expressed (DEGs) is critical step in transcriptome analysis. However, current methods, including Gene Ontology analysis and manual annotation, essentially rely on existing knowledge, which highly biased depending the extent literature. As result, understudied genes, some may be associated with important molecular mechanisms, are often ignored or remain obscure. To address this problem, we propose Clover, data‐driven scoring method to specifically highlight genes. Clover aims prioritize mechanisms by integrating three metrics: likelihood appearing DEG list, tissue specificity, number publications. We applied Alzheimer's disease data confirmed that it successfully detected known Moreover, effectively prioritized but potentially druggable Overall, our offers novel approach gene characterization has potential expand understanding functions. an open‐source software written Python3 available GitHub at https://github.com/G708/Clover .

Language: Английский

Clover: An unbiased method for prioritizing differentially expressed genes using a data‐driven approach DOI Creative Commons
Gina Miku Oba, Ryuichiro Nakato

Genes to Cells, Journal Year: 2024, Volume and Issue: 29(6), P. 456 - 470

Published: April 11, 2024

Abstract Identifying key genes from a list of differentially expressed (DEGs) is critical step in transcriptome analysis. However, current methods, including Gene Ontology analysis and manual annotation, essentially rely on existing knowledge, which highly biased depending the extent literature. As result, understudied genes, some may be associated with important molecular mechanisms, are often ignored or remain obscure. To address this problem, we propose Clover, data‐driven scoring method to specifically highlight genes. Clover aims prioritize mechanisms by integrating three metrics: likelihood appearing DEG list, tissue specificity, number publications. We applied Alzheimer's disease data confirmed that it successfully detected known Moreover, effectively prioritized but potentially druggable Overall, our offers novel approach gene characterization has potential expand understanding functions. an open‐source software written Python3 available GitHub at https://github.com/G708/Clover .

Language: Английский

Citations

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