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Many of these pathways and the associated regulatory mechanisms might be obscured by a large number of other significant processes and thus not identified as significant by standard gene set enrichment analysis tools.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We present a novel method called Independent Enrichment Analysis (IEA) and software TAFFEL that eases the task by clustering genes to subgroups using Gene Ontology categories and transcription regulators. IEA indicates transcriptional regulators putatively controlling biological functions in studied condition.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>We demonstrate that the developed method and TAFFEL tool give new insight to the analysis of differentially expressed genes and can generate novel hypotheses. Our comparison to other popular methods showed that the IEA method implemented in TAFFEL can find important biological phenomena, which are not reported by other methods.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-171","type":"journal-article","created":{"date-parts":[[2011,5,19]],"date-time":"2011-05-19T19:03:20Z","timestamp":1305831800000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["TAFFEL: Independent Enrichment Analysis of gene sets"],"prefix":"10.1186","volume":"12","author":[{"given":"Mitja I","family":"Kurki","sequence":"first","affiliation":[]},{"given":"Jussi","family":"Paananen","sequence":"additional","affiliation":[]},{"given":"Markus","family":"Storvik","sequence":"additional","affiliation":[]},{"given":"Seppo","family":"Yl\u00e4-Herttuala","sequence":"additional","affiliation":[]},{"given":"Juha E","family":"J\u00e4\u00e4skel\u00e4inen","sequence":"additional","affiliation":[]},{"given":"Mikael","family":"von und zu Fraunberg","sequence":"additional","affiliation":[]},{"given":"Garry","family":"Wong","sequence":"additional","affiliation":[]},{"given":"Petri","family":"Pehkonen","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,5,19]]},"reference":[{"issue":"1","key":"4566_CR1","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/75556","volume":"25","author":"M Ashburner","year":"2000","unstructured":"Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G: Gene ontology: tool for the unification of biology. 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