We highlight here a number of key issues that emerged, enriched by our experiences over the last decade by working with a variety of stakeholders, including researchers, bioinformaticians, developers in public and private sectors, standards-developing communities, as well as funders and publishers.
In Step 1, lines (6) to (9), we find the emerging substrings enriched in the test set; then lines (10) to (15) are the step to construct the PWM and the intramotif distribution for each emerging substring.
In the process of developing these methodologies, a number of important facets, often not the key focus of previous publications, have emerged to enrich our understanding and guide our exploration.
This applies especially to plasma/serum, and therefore techniques have emerged to enrich and study subproteomes to reduce the complexity and to be able to detect low abundant proteins [ 89, 90].
Two gene sets emerged as strongly enriched in tumors with pCR to chemotherapy in both ER+ and ER- tumors.
A pertinent cluster to our study that emerged is one enriched for genes involved in developmental processes.
Similarly, most of the molecular functional categories that emerged as significantly enriched are also groups of genes that participate in metabolic processes, e.g., exo- and metallopeptidases, hydrolases, and genes coding for o-methyltransferases, and carrier proteins (Table 3).
Upon ESC differentiation, most of these binding sites disappear and instead new CTCF independent RAD21 binding sites emerge, which are enriched for binding sites of transcription factors implicated in early differentiation.
The fact that these sites disappear in EBs and new binding sites emerge, which are enriched for early developmental transcription factors suggests that these sites are functionally relevant for the execution of developmental expression programs.
This study showed that both predictable and less-predictable pathways emerge as highly enriched for CIN genes.
When enrichment analysis was applied to this set of genes, five functional annotation clusters emerged; the most highly enriched was a cluster of immunoglobulin-like molecules with an enrichment score of 13.13.
