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Table 4 Comparison of the qualitative and quantitative behaviors of the network “perturbation” to the expected behavior in the various datasets and studies

From: Quantification of biological network perturbations for mechanistic insight and diagnostics using two-layer causal models

Category Gene-level Enrichment 28-day rat inhalation 28-day rat inhalation RLAK study RLAK study CDKi study Complete match with
  statistics statistics TNF-IL1-NFKB xenobiotic TNF-IL1-NFKB Xenobiotic cell cycle biological expectations
Forward FCS t mean ×/ ×/ /() ./ × ×/ 0
maxmean ×/ × ()/ ×/ × ./ × ×/ 0
GSEA ×/ × ×/ ×/() ./() ×/ 0
fc mean ()/ ()/ ()/ ./ × ×/ 0
maxmean / / ()/() ./ × ×/ 2
GSEA ×/ ×/ ×/() ./ × ×/ 0
Backward ORA fdr RCR ×/ × / × ×/ × ./ / × 1
Backward FCS t mean ×/ × ×/ ×/ × ./ /() 1
  maxmean ×/ × ×/() ×/ × ./ / × 1
t GSEA ×/ × ×/ ×/ × ./ / × 1
fc mean ()/() /() /() ./ /() 1
maxmean / / × / ./ /() 3
GSEA ×/ ×/ ×/ × ./ / × 1
NPA ()/ na / na na 1
Backward PT fc TopoNPA / / / ./ / 5
  1. A indicates that the result corresponds to the biological expectation, a () indicate that up to one exception it matches the expectation, a × indicates that it does not match the expectation, and “.” means that the aspect is unimportant in the case-study. Finally, “na” indicates that the method does not apply. Each use case is assessed for its quantitative (the first symbol) and its qualitative (second symbol) aspects. The comparison scheme is discussed in the material and methods and the table is derived from Figures S1-S5. Overall, TopoNPA behaves as expected and is the only method fully matching the expectations.