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Table 3 Ranking improvement for cancer-related KEGG signaling pathways with DS

From: THINK Back: KNowledge-based Interpretation of High Throughput data

Dataset #Pways GSA-DS LRpath-DS GSEA-DS
   0 - 10 > 10 TOTAL 0 - 10 > 10 TOTAL 0 - 10 > 10 TOTAL
Breast GSE-2990 18 8 5 13 7 8 15 6 7 13
Breast GSE-3494 18 9 5 14 8 5 13 10 5 15
Lung Boston 18 4 4 8 4 9 13 5 6 11
Lung Michigan 18 6 7 13 4 6 10 7 7 14
AVERAGE 7 5 12 6 7 13 7 6 13
  1. This table presents the summary of improvement in rankings for 19 cancer-related KEGG signaling pathways, when using the DS-adjusted methods. We can observe that out of these 19 cancer-related pathways, DS-adjusted methods improve the rankings of more than half of the pathways, with LRpath-DS showing average improvements in the rankings of 78% of the mentioned signaling pathways. We also differentiate between large ranking improvements (greater than 10 ranks), and observe that GSEA-DS has an average rank improvement greater than ten ranks in 69% of the studied pathways.