M6adecom: Analysis of M6a Profile Matrix Based on Graph Regularized Non-Negative Matrix Factorization.

Epitranscriptomic m6A methylation is shown to mediate extensive regulations under the context of various RNA binding protein (RBP) readers. With m6A methylation data has reached a sizable scale, the functional context-aware analysis of m6A profiles is becoming more feasible and demanded. In this study, we employed graph regularized non-negative matrix factorization (GNMF) for m6A profile analysis and comparison, where the RBP binding preference of m6A sites were incorporated as the functional context-based graph constraint term. Compared to the baseline non-negative matrix factorization (NMF) method, this GNMF-based method could better capture the distinctions in multiple functional characteristics between different group of m6A sites, including but not limited to the associated biological pathways and disease genes. We further established m6Adecom, an online tool that can be used for correlation and enrichment analysis of m6A profiles using the matrix decomposition result from GNMF, and gene set enrichment analysis based on the high-score m6A sites. m6Adecom is freely accessible at http://www.rnanut.net/m6adecom.