A practical problem of GEA is that a given gene set which is not significantly overlapping a KEGG pathway, may be significant, with the same overlap, to the same pathway in e.g.
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A novel method for crosstalk analysis of biological networks: improving accuracy of pathway annotation.
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The sentences
One of the pathways BinoX identified as having a highly significant crosstalk with the cancer gene set was the Neurotrophin Signaling pathway.