Sentence examples for set ranked from inspiring English sources
Although PEBP (CBFb) was only marginally enriched (p∼0.1) in this list, it appeared among the ten top TFBSs exhibiting the lowest p-values both in the lists derived by DEMON from consensus data sets (ranked 2nd and 3rd) and from the hIPCs vs. PANC-1 cells experiment data set (ranked 6th).
The gene sets of the Balko, and Chen but not of the Larsen signature showed statistically significant enrichment at the top of data set ranked by survival.
The output of the pipeline consists of a non-redundant ranking of GO BP terms overrepresented in the input set, ranked according to their Bonferroni-corrected p-values.
The high and low gene expression groups were identified by considering the top and bottom 10% of genes in the data set ranked by expression level (percentile method).
NES represents the enrichment of genes in the designated GSEA gene set, ranked according to the overrepresentation of genes at the top or bottom of the list, normalized to gene set size.
In a second approach, GSEA was employed to test for enrichment of the signature components at the top of the total data set, ranked according to differential expression of genes between long-term and short-term survival.
The rank-based method consistently prioritized PI3K gene sets; with the KEGG phosphatidylinositol signaling system gene set ranking first along with many additional PI3K/ERBB related gene sets (Additional file 1: Table S5).
When top ranked gene sets from both methods, based on FDR for association and the AUC value for ROC-based classification, were combined by averaging the top gene set ranks, there was a significant overlap between the gene sets ranked by both methods (Spearman rank correlation over all gene sets = 0.96, p-value < 10-16 ; Additional File 6).
Three CTD-based fibrate gene sets ranked within the top-10 significant results in ToxProfiler and GeneCodis (using the single annotation option in GeneCodis) (Table 2).
The next-gen TM fibrate gene sets ranked much lower when using the weighted global test compared to the other tools.
The CTD-based gene sets ranked highest when using the GeneCodis single annotation option (Table 1), but for some data sets the gene set representing the treatment did not score significant.
