LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights.

Since for most methods each gene set is tested independently, there may be significant redundancy among enriched gene sets, making it difficult for biologists to interpret the results.

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The yeast TF network is a small network, and network perturbations on this network have significant impacts on LEGO’s performance: both the cell cycle and the sporulation GO term are barely significant after 10% edge removal or rewiring, and their average ranks drops with the increase of network perturbations ( Supplementary Fig.

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