Table 2 Comparison of the properties of several geneset differential expression analysis methods
Author | Year | Hypothesis | Data used | Group statistic | Significance | Name | Properties | Individual statistic |
|---|---|---|---|---|---|---|---|---|
Mootha et al | 2003 | Competitive | Individual statistic | ES (Running Sum) | Sample permutations | GSEA | Hybrid | Signal/noise Ratio |
Subramanian et al | 2005 | Competitive | Individual statistic | ES (Running Sum) | Sample permutations | GSEA | Hybrid, asymmetrical | Individual correlation (r) |
Keller et al | 2007 | Competitive | Individual statistic | ES (Running Sum) | Competitive theoretical model | Variant GSEA | Hybrid, symmetrical | * |
Effron & Tibshirani | 2007 | Competitive | Individual statistic | ES (Running Sum) | Sample permutations | GSA | Restandardizaton | * |
Pavlidis et al | 2004 | Competitive | Individual statistic | Log (p(g)) = mean[log[p(i)]] | Genes permutations | Depends on the geneset size | Pearson correlation coef. | |
Tian et al | 2005 | Competitive | Individual statistic | Weighted mean | Genes permutations | Standardization | Student t | |
Tian et al | 2005 | Self-contained | Individual statistic | Weighted mean | Sample permutations | Standardization | Student t | |
Kim & Volsky | 2005 | Self-contained | Individual statistic | Mean | Normal distribution | PAGE | Central Limit Theorem | Fold-change |
Effron & Tibshirani | 2007 | Self-contained | Individual statistic | Mean | Sample permutations | GSA | Unidirectional + Restandardization | Student t |
Effron & Tibshirani | 2007 | Self-contained | Individual statistic | Maxmean | Sample permutations | GSA | Unidirectional (directional subset) + Restandardization | Student t |
Effron & Tibshirani | 2007 | Self-contained | Individual statistic | Absmean | Sample permutations | GSA | Unidirectional (absolute value) + Restandardization | Student t |
Dinu et al | 2007 | Self-contained | Expression data | Sum (d2) | Sample permutations | SAM-GS | Determination of S0 | SAM d statistic |
Goeman et al | 2004 | Self-contained | Expression data | Q(g) = mean(Q(i)) | Permutation/Gamma/Asymptotic | GlobalTest | P (Y|X) | Q(i) |
Mansmann & Meister | 2005 | Self-contained | Expression data | F | Sample permutations | GlobalAncova | P (X|Y) | |
Berger et al | Unpublished | Self-contained | Expression data | F | Fisher F | ANOVA-2 | Unidirectional | |
Berger et al | Unpublished | Self-contained | Expression data | F* | Sample permutations/random data | FAERI | Bidirectional |