title: TAFFEL: Independent Enrichment Analysis of gene sets.
abstract: BACKGROUND
  A major challenge in genomic research is identifying significant biological processes and generating new hypotheses from large gene sets. Gene sets often consist of multiple separate biological pathways, controlled by distinct regulatory mechanisms. 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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors: Department of Biosciences, University of Eastern Finland, PO Box 1627, FIN-70211 Kuopio, Finland.
authors: Mitja I
authors: MI
authors: Kurki
authors: Jussi
authors: J
authors: Paananen
authors: Markus
authors: M
authors: Storvik
authors: Seppo
authors: S
authors: Ylä-Herttuala
authors: Juha E
authors: JE
authors: Jääskeläinen
authors: Mikael
authors: M
authors: von Und Zu Fraunberg
authors: Garry
authors: G
authors: Wong
authors: Petri
authors: P
authors: Pehkonen
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