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Genetic network inference: the effects of preprocessing
University of Skövde, Department of Computer Science.
University of Skövde, Department of Computer Science.ORCID iD: 0000-0001-6254-4335
2003 (English)In: Biosystems (Amsterdam. Print), ISSN 0303-2647, E-ISSN 1872-8324, Vol. 72, no 3, p. 229-239Article in journal (Refereed) Published
Abstract [en]

Clustering of gene expression data and gene network inference from such data has been a major research topic in recent years. In clustering, pairwise measurements are performed when calculating the distance matrix upon which the clustering is based. Pairwise measurements can also be used for gene network inference, by deriving potential interactions above a certain correlation or distance threshold. Our experiments show how interaction networks derived by this simple approach exhibit low—but significant—sensitivity and specificity. We also explore the effects that normalization and prefiltering have on the results of methods for identifying interactions from expression data. Before derivation of interactions or clustering, preprocessing is often performed by applying normalization to rescale the expression profiles and prefiltering where genes that do not appear to contribute to regulation are removed. In this paper, different ways of normalizing in combination with different distance measurements are tested on both unfiltered and prefiltered data, different prefiltering criteria are considered.

Place, publisher, year, edition, pages
Elsevier, 2003. Vol. 72, no 3, p. 229-239
Identifiers
URN: urn:nbn:se:his:diva-1489DOI: 10.1016/S0303-2647(03)00164-3ISI: 000187240500004PubMedID: 14643491Scopus ID: 2-s2.0-0345688074OAI: oai:DiVA.org:his-1489DiVA, id: diva2:31765
Available from: 2007-07-02 Created: 2007-07-02 Last updated: 2019-01-28Bibliographically approved

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Lindlöf, AngelicaOlsson, Björn

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