Table 2.
Type | Method | Query | Ref | Publications |
---|---|---|---|---|
Aggregation-based |
eXtreme Sum (XS) | or | Cheng et al. 2014 | |
eXtreme Mean | or | |||
T-statistic (TS) | Tian et al. 2005; Goeman et al. 2004, 2005 | |||
Ranksum statistic (RS) | Barry, Nobel, and Wright 2005; Gower, Spira, and Lenburg 2011 | |||
GSEAa | Mootha et al. 2003 | |||
GSEAb | Subramanian et al. 2005 | |||
GSEAc | Subramanian et al. 2007 | |||
Total enrichment score (TES) | Iorio, Tagliaferri, and Bernardo 2009 | |||
Vector-based |
Pearson correlation | or | or | Tenenbaum et al. 2008 |
Spearman Correlation | or | or | Tanner and Agarwal 2008; Zhang et al. 2009 | |
Cosine | or | or | Cheng et al. 2012 | |
Jaccard index (JI) | ||||
Signed Jaccard (SJI) | Zichen Wang et al. 2016 |