Sentence examples for modules for enrichment from inspiring English sources

Due to mutational heterogeneity, current analyses are often restricted to known pathways and functional modules for enrichment of somatic mutations.

TFBS enrichment analysis was conducted by scanning the promoter sequence of the genes in the analyzed modules for enrichment of known transcription factor binding motifs using the Clover algorithm [ 52].

We tested the Wigwams modules for enrichment of known TF binding motifs and found that 51 of the 78 modules had at least one overrepresented motif (Supplementary Dataset S5), suggesting that the module members were co-regulated.

Finally, we describe the integration of our GWAS and gene expression analyses, where we performed eSNP analysis to assess for the association between genetic variation and gene expression, assessed GWAS loci for eSNPs, identified coexpression modules tagged by GWAS loci, and analyzed coexpression modules for enrichment of allergic-rhinitis associated eSNPs [ 15].

To assist with the categorisation of co-expressed genes and partitioned modules according to their potential function or processes, we assessed the modules for enrichment primarily for GO terms in R (http://www.r-project.org) using the 'gProfileR' package [ 37] to interface g:profiler (http://gprofiler.at.mt.ut.ee/gprofiler/).ee/gprofiler/

Zinc finger, inflammatory response, and immunoglobulin domain were other pathways highlighted by examining the coexpression modules for functional enrichment.

We then assessed these modules for their enrichment of PrCa candidate genes collected by eQTLs, SCNA, somatic mutation data, or prognostic studies using the hypergeometric test.

We assigned Gene Ontology classifications to modules by testing for enrichment at GO nodes using a hyper-geometric distribution and a 0.01 p-value threshold.

We used the EASE (Expression Analysis Systematic Explorer) analysis implemented in DAVID functional annotation tool http://david.niaid.nih.gov/david/ease.htm[ 41, 42] to analyze the candidate genes contained within each module for functional enrichment.

DAVID software (http://david.abcc.ncifcrf.gov/) was used to test each module for genome enrichment in GO process terms, PIR superfamily, Panther or Kegg pathways, InterPro or SwissProt keywords, and to test IA genes having an impact on overall survival (Fisher's exact tests with Benjamini-Hochberg correction for multiple testing).

More details on the network construction and module identification can be found in Additional File 3. The modules were then searched for enrichment of known biological pathways in MSigDB [ 22].