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Gene expression profiling – Clusters of possibilities

Bergkvist, Anders ; Rusnakova, Vendula ; Sindelka, Radek ; Garda, Jose Manuel Andrade ; Sjögreen, Björn ; Lindh, Daniel ; Forootan, Amin ; Kubista, Mikael

Methods (San Diego, Calif.), 2010-04, Vol.50 (4), p.323-335 [Periódico revisado por pares]

United States: Elsevier Inc

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Título:
Gene expression profiling – Clusters of possibilities
Autor: Bergkvist, Anders ; Rusnakova, Vendula ; Sindelka, Radek ; Garda, Jose Manuel Andrade ; Sjögreen, Björn ; Lindh, Daniel ; Forootan, Amin ; Kubista, Mikael
Assuntos: Algorithms ; Animals ; Cluster Analysis ; Embryo, Nonmammalian ; Female ; Fertilization in Vitro ; Gene Expression Profiling - methods ; Heatmap ; Hierarchical clustering ; Hypotheses ; Male ; PCA ; Principal Component Analysis ; qPCR ; SOM ; Statistical analysis ; Statistics as Topic ; Xenopus laevis ; Xenopus laevis - embryology ; Xenopus laevis - genetics ; Xenopus laevis - growth & development
É parte de: Methods (San Diego, Calif.), 2010-04, Vol.50 (4), p.323-335
Notas: ObjectType-Article-2
SourceType-Scholarly Journals-1
ObjectType-Feature-3
content type line 23
ObjectType-Review-1
Descrição: Advances in qPCR technology allow studies of increasingly large systems comprising many genes and samples. The increasing data sizes allow expression profiling both in the gene and the samples dimension while also putting higher demands on sound statistical analysis and expertise to handle and interpret its results. We distinguish between exploratory and confirmatory statistical studies. In this paper we demonstrate several techniques available for exploratory studies on a system of Xenopus laevis development from egg to tadpole. Techniques include hierarchical clustering, heatmap, principal component analysis and self-organizing maps. We stress that even though exploratory studies are excellent for generating hypotheses, results have not been proven statistically significant until an independent confirmatory study has been performed. An exploratory study may certainly be valuable in its own right, and there are often not enough resources to report both an exploratory and a confirmatory study at the same time. However, exploratory and confirmatory studies are intimately connected and we would like to raise that awareness among qPCR practitioners. We suggest that scientific reports should always have a hypothesis focus. Reports are either hypothesis generating, from an exploratory study, or hypothesis validating, from a confirmatory study, or both. In either case, we suggest the generated or validated hypotheses be specifically stated.
Editor: United States: Elsevier Inc
Idioma: Inglês

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Gene expression profiling – Clusters of possibilities

Bergkvist, Anders ; Rusnakova, Vendula ; Sindelka, Radek ; Garda, Jose Manuel Andrade ; Sjögreen, Björn ; Lindh, Daniel ; Forootan, Amin ; Kubista, Mikael

United States: Elsevier Inc

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