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TAFFEL: Independent Enrichment Analysis of gene sets
Kurki M.I.1; Paananen J.1; Storvik M.1; Yla-Herttuala S.1; Jaaskelainen J.E.2; von und zu Fraunberg M.2; Wong G.1; Pehkonen P.1
2011-05-19
Source PublicationBMC Bioinformatics
ISSN14712105
Volume12
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. © 2011 Kurki et al; licensee BioMed Central Ltd.

DOI10.1186/1471-2105-12-171
URLView the original
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS SubjectBiochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS IDWOS:000291931300001
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Cited Times [WOS]:2   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionFaculty of Health Sciences
Affiliation1.Itä-Suomen yliopisto
2.Kuopio University Hospital
Recommended Citation
GB/T 7714
Kurki M.I.,Paananen J.,Storvik M.,et al. TAFFEL: Independent Enrichment Analysis of gene sets[J]. BMC Bioinformatics,2011,12.
APA Kurki M.I..,Paananen J..,Storvik M..,Yla-Herttuala S..,Jaaskelainen J.E..,...&Pehkonen P..(2011).TAFFEL: Independent Enrichment Analysis of gene sets.BMC Bioinformatics,12.
MLA Kurki M.I.,et al."TAFFEL: Independent Enrichment Analysis of gene sets".BMC Bioinformatics 12(2011).
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