Sentence examples for module enrichment analysis from inspiring English sources

To test whether this module is significantly enriched with mutated genes, we performed network module enrichment analysis for the 92 significantly mutated genes (Fig. 4g), and the AKAP12 containing module was one of four enriched modules (Fig. 4h, FDR = 0.006, enrichment ratio = 8.6).

In this module, enrichment analysis results were provided after integrating and matching the significantly enriched PTM terms of the two lists of proteins.

For a gene signature, we first perform a module enrichment analysis using a hypergeometric test.

Functional enrichments of each cluster were then evaluated by module enrichment analysis [ 12] of its gene members, and illustrated using Cytoscape software [ 13] as illustrated in Figure  3.

In addition to the network modules, enrichment analysis can also be performed against the GO or pathway gene sets.

Others have looked for tissue-specific cis-regulatory modules by enrichment analysis for motifs discovered de novo in tissue-specific promoters relative to other promoters from the same species [ 21].

Based on miRNA-gene regulations, given one miRNA, a module will be regarded to be regulated by this miRNA if its target genes are significantly enriched in this module, where the enrichment analysis was conducted with Fisher exact test with P-value cutoff of 0.01.

Here, we investigated every module by GO/KEGG enrichment analysis and performed over-representation analysis with respect to curated disease associated genes (Methods).

To determine which cell types could have contributed to the detected gene expression changes and coexpression patterns in each module, cell-type enrichment analysis was conducted as described by Ponomarev and collaborators [ 15].

To investigate the disturbed pathways of these NM and M modules, we conducted enrichment analysis on genes from each of the key regulatory modules with all non-metabolic KEGG resource containing gene regulatory and signaling pathways.

Based on a list of genes loaded from a file, the user can construct a sub-network, perform network clustering to search for network modules related to patient clinical or other phenotypic information, annotate network modules, perform pathway enrichment analysis, and even model pathway activities based on probabilistic graphical models.