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Over-representation analysis software tools | High-throughput sequencing

The immediate need for functional analysis of microarray gene expression data and the emergence of GO during that period gave rise to over-representation analysis (ORA), which statistically evaluates the fraction of genes in a particular pathway found among the set of genes showing changes in expression. It is also referred to as “2×2 table method” in the literature (Goeman and Buhlmann, 2007).

References:
(Goeman and Buhlmann, 2007) Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics.

Source text:
(Khatri et al., 2012) Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol.

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