## Results
### Biological Processes  
Genes identified by TD-based unsupervised FE seem to successfully identify TFs recruited by m6A. It is more interesting to know the kind of biological processes that are mediated by those identified genes. For that, we investigated the \"KEGG 2019 Human\" category in Enrichr (full list is available in Supplementary Materials). This category is a list of genes included in the pathways that Kyoto Encyclopedia of Genes and Genomes (KEGG) [44] provided. KEGG is a collection of pathways that are experimentally validated. Based upon the biological considerations, various pathways are identified, along with genes and compounds that take part in individual pathways. There are six KEGG pathways commonly selected (Figure 7 and Table 7), which also suggest the success of TD-based unsupervised FE, since it is unlikely that there are significant overlaps between pathways selected using two independent datasets. \begin{table}
\begin{tabular}{l c c c c} \hline \hline
**Pathway Name** & **Found** & **Ratio** & \(\boldsymbol{p}\)**-Value** & **FDR** \\ \hline Transcriptional regulation of pluripotent stem cells & \(13/45\) & \(3.00\times 10^{-3}\) & \(1.11\times 10^{-16}\) & \(3.76\times 10^{-14}\) \\ Developmental Biology & \(23/1241\) & \(8.50\times 10^{-2}\) & \(2.35\times 10^{-12}\) & \(3.97\times 10^{-10}\) \\ Generic Transcription Pathway & \(24/1554\) & \(1.06\times 10^{-1}\) & \(2.99\times 10^{-11}\) & \(3.38\times 10^{-9}\) \\ POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation & \(6/21\) & \(1.00\times 10^{-3}\) & \(1.29\times 10^{-10}\) & \(1.01\times 10^{-8}\) \\ Gene expression (Transcription) & \(25/1851\) & \(1.26\times 10^{-1}\) & \(1.67\times 10^{-10}\) & \(1.01\times 10^{-8}\) \\ RNA Polymerase II Transcription & \(24/1693\) & \(1.15\times 10^{-1}\) & \(1.80\times 10^{-10}\) & \(1.01\times 10^{-8}\) \\ Interleukin-4 and Interleukin-13 signaling & \(9/211\) & \(1.40\times 10^{-2}\) & \(3.87\times 10^{-8}\) & \(1.86\times 10^{-6}\) \\ ESR-mediated signaling & \(9/256\) & \(1.70\times 10^{-2}\) & \(1.97\times 10^{-7}\) & \(8.26\times 10^{-6}\) \\ Estrogen-dependent gene expression & \(7/154\) & \(1.00\times 10^{-2}\) & \(9.44\times 10^{-7}\) & \(3.49\times 10^{-5}\) \\ Transcriptional regulation of granulopoiesis & \(5/71\) & \(5.00\times 10^{-3}\) & \(4.69\times 10^{-6}\) & \(1.33\times 10^{-4}\) \\ Signaling by Nuclear Receptors & \(9/385\) & \(2.60\times 10^{-2}\) & \(5.57\times 10^{-6}\) & \(1.33\times 10^{-4}\) \\ POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation & \(3/10\) & \(6.82\times 10^{-4}\) & \(6.06\times 10^{-6}\) & \(1.33\times 10^{-4}\) \\ Binding of TCF/LEF:CTNNB1 to target gene promoters & \(3/10\) & \(6.82\times 10^{-4}\) & \(6.06\times 10^{-6}\) & \(1.33\times 10^{-4}\) \\ Activation of PUMA and translocation to mitochondria & \(3/10\) & \(6.82\times 10^{-4}\) & \(6.06\times 10^{-6}\) & \(1.33\times 10^{-4}\) \\ RUNX3 regulates WNT signaling & \(3/10\) & \(6.82\times 10^{-4}\) & \(6.06\times 10^{-6}\) & \(1.33\times 10^{-4}\) \\ Repression of WNT target genes & \(3/16\) & \(1.00\times 10^{-3}\) & \(2.45\times 10^{-5}\) & \(5.14\times 10^{-4}\) \\ Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors & \(4/52\) & \(4.00\times 10^{-3}\) & \(3.19\times 10^{-5}\) & \(6.06\times 10^{-4}\) \\ TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle & \(3/20\) & \(1.00\times 10^{-3}\) & \(4.73\times 10^{-5}\) & \(8.44\times 10^{-4}\) \\ Signaling by Interleukins & \(10/639\) & \(4.40\times 10^{-2}\) & \(5.07\times 10^{-5}\) & \(8.44\times 10^{-4}\) \\ Transcriptional regulation by RUNX3 & \(5/118\) & \(8.00\times 10^{-3}\) & \(5.27\times 10^{-5}\) & \(8.44\times 10^{-4}\) \\ TFAP2 (AP-2) family regulates transcription of growth factors & \(3/21\) & \(1.00\times 10^{-3}\) & \(5.46\times 10^{-5}\) & \(8.74\times 10^{-4}\) \\ and their receptors & & & & \\ Intrinsic Pathway for Apoptosis & \(4/61\) & \(4.00\times 10^{-3}\) & \(5.90\times 10^{-5}\) & \(8.86\times 10^{-4}\) \\ \hline \hline \end{tabular}
\end{table}