Advances in cancer DNA methylation analysis with methPLIER: use of non-negative matrix factorization and knowledge-based constraints to enhance biological interpretability.

Among the genes that showed a trend toward hypermethylation in the pan-negative cases were RUNX3 , a known tumor suppressor gene, and CCNA1 44 , which has been reported to correlate with treatment response to doxorubicin and 5-fluorouracil (Fig. 6c, d ).

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