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. Author manuscript; available in PMC: 2023 Nov 21.
Published in final edited form as: Chem Res Toxicol. 2022 Oct 27;35(11):1929–1949. doi: 10.1021/acs.chemrestox.2c00245

Table 2.

Summary of connectivity mapping methods

Type Method Query Ref Publications
Aggregation-based
  SMa
eXtreme Sum (XS) Sq xr or xrn Cheng et al. 2014
eXtreme Mean Sq xr or xrn
T-statistic (TS) Sq xr Tian et al. 2005; Goeman et al. 2004, 2005
Ranksum statistic (RS) Sq xr Barry, Nobel, and Wright 2005; Gower, Spira, and Lenburg 2011
GSEAa xq Sr Mootha et al. 2003
GSEAb xq Sr Subramanian et al. 2005
GSEAc DSq xr Subramanian et al. 2007
Total enrichment score (TES) DSq xr Iorio, Tagliaferri, and Bernardo 2009
Vector-based
  SMv
Pearson correlation xq or xqn xr or xrn Tenenbaum et al. 2008
Spearman Correlation xq or xqn xr or xrn Tanner and Agarwal 2008; Zhang et al. 2009
Cosine xq or xqn xr or xrn Cheng et al. 2012
Jaccard index (JI) Sq Sr
Signed Jaccard (SJI) Sq+,Sq Sr+,Sr Zichen Wang et al. 2016