TAFFEL: Independent Enrichment Analysis of gene sets

BMC Bioinformatics

Methodology Article

Petri Pehkonen¹  Markus Storvik²  Seppo Ylä-Herttuala³  Juha E Jääskeläinen⁴  Mikael von und zu Fraunberg⁴  Garry Wong⁵  Mitja I Kurki⁶  Jussi Paananen⁷ 

[1] Department of Biosciences, University of Eastern Finland, PO Box 1627, FIN-70211, Kuopio, Finland;Department of Biosciences, University of Eastern Finland, PO Box 1627, FIN-70211, Kuopio, Finland;Department of Pharmacology and Toxicology, University of Eastern Finland, PO Box 1627, FIN-70211, Kuopio, Finland;Department of Biotechnology and Molecular Medicine, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211, Kuopio, Finland;Department of Neurosurgery, Kuopio University Hospital, FIN-70211, Kuopio, Finland;Laboratory of Functional Genomics and Bioinformatics, Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211, Kuopio, Finland;Department of Biosciences, University of Eastern Finland, PO Box 1627, FIN-70211, Kuopio, Finland;Laboratory of Functional Genomics and Bioinformatics, Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211, Kuopio, Finland;Department of Biosciences, University of Eastern Finland, PO Box 1627, FIN-70211, Kuopio, Finland;Department of Neurosurgery, Kuopio University Hospital, FIN-70211, Kuopio, Finland;Laboratory of Functional Genomics and Bioinformatics, Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, PO Box 1627, FIN-70211, Kuopio, Finland;Institute of Clinical Medicine, University of Eastern Finland, PO Box 1627, FIN-70211, Kuopio, Finland;

关键词: Gene Ontology;    Forskolin;    Differentially Express;    Differentially Express Gene;    Cluster Solution;   

DOI  :  10.1186/1471-2105-12-171

 received in 2011-01-19, accepted in 2011-05-19,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundA 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.ResultsWe 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.ConclusionsWe 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.

【 授权许可】

Unknown   
© Kurki et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.