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TAFFEL: Independent Enrichment Analysis of gene sets
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 associa...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120704/ https://www.ncbi.nlm.nih.gov/pubmed/21592412 http://dx.doi.org/10.1186/1471-2105-12-171 |
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author | Kurki, Mitja I Paananen, Jussi Storvik, Markus Ylä-Herttuala, Seppo Jääskeläinen, Juha E von und zu Fraunberg, Mikael Wong, Garry Pehkonen, Petri |
author_facet | Kurki, Mitja I Paananen, Jussi Storvik, Markus Ylä-Herttuala, Seppo Jääskeläinen, Juha E von und zu Fraunberg, Mikael Wong, Garry Pehkonen, Petri |
author_sort | Kurki, Mitja I |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3120704 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-31207042011-06-23 TAFFEL: Independent Enrichment Analysis of gene sets Kurki, Mitja I Paananen, Jussi Storvik, Markus Ylä-Herttuala, Seppo Jääskeläinen, Juha E von und zu Fraunberg, Mikael Wong, Garry Pehkonen, Petri BMC Bioinformatics Methodology Article 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. BioMed Central 2011-05-19 /pmc/articles/PMC3120704/ /pubmed/21592412 http://dx.doi.org/10.1186/1471-2105-12-171 Text en Copyright ©2011 Kurki et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 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. |
spellingShingle | Methodology Article Kurki, Mitja I Paananen, Jussi Storvik, Markus Ylä-Herttuala, Seppo Jääskeläinen, Juha E von und zu Fraunberg, Mikael Wong, Garry Pehkonen, Petri TAFFEL: Independent Enrichment Analysis of gene sets |
title | TAFFEL: Independent Enrichment Analysis of gene sets |
title_full | TAFFEL: Independent Enrichment Analysis of gene sets |
title_fullStr | TAFFEL: Independent Enrichment Analysis of gene sets |
title_full_unstemmed | TAFFEL: Independent Enrichment Analysis of gene sets |
title_short | TAFFEL: Independent Enrichment Analysis of gene sets |
title_sort | taffel: independent enrichment analysis of gene sets |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3120704/ https://www.ncbi.nlm.nih.gov/pubmed/21592412 http://dx.doi.org/10.1186/1471-2105-12-171 |
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