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Table 6 Pathway recovery (over-representation of enriched pathways from causal reasoning nodes in the set of compound target-associated pathways expressed as a − log10(p-value)) averaged for each parameter level for the benchmark results for compound Diethylstilbestrol

From: Benchmarking causal reasoning algorithms for gene expression-based compound mechanism of action analysis

Platform

Gene Set

Cell Line

Algorithm

Network

LINCS

26.5

ALL

24.3

MCF7

24.9

CausalR (Results table)

4.33

Omnipath

36.7

CMap

23.8

LM

27.0

PC3

25.5

CARNIVAL

15.9

Metabase_All

21.5

  

BING

24.2

  

CausalR (Network)

34.6

Metabase_High

20.6

      

SigNet

46.0

Metabase_Med

22.0

Range

2.70

 

2.77

 

0.59

 

41.6

 

16.2

  1. The range across parameter levels is given in bold
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BMC Bioinformatics

ISSN: 1471-2105

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