Analysis of the real EADGENE data set: Multivariate approaches and post analysis (Open Access publication)
| Autor: | Agnès Bonnet, Hans-Joachim Schuberth, Wei Yang, Wolfram Petzl, Hans-Martin Seyfert, Haisheng Nie, Henrik Hornshøj, M.H. Pool, Evert M. van Schothorst, Bart Buitenhuis, Sébastien Déjean, Liz Glass, Dirk-Jan de Koning, Florence Jaffrézic, Peter Sørensen, Holm Zerbe, Gwenola Tosser-Klopp, Mogens Sandø Lund, Kirsty Jensen, Mylène Duval, Céline Delmas, Li Jiang, Kim-Anh Lê Cao, Jakob Hedegaard, Christèle Robert-Granié, Ina Hulsegge, Magali San Cristobal, Michael Watson, R. Closset, D. Waddington |
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| Přispěvatelé: | Revues Inra, Import |
| Jazyk: | angličtina |
| Rok vydání: | 2007 |
| Předmět: |
Multivariate statistics
Multivariate analysis lcsh:QH426-470 bovine microarray Biological database [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics Biology mastitis gene set analysis multivariate approaches bovine annotation Bioconductor 03 medical and health sciences Genetics Genetics(clinical) Gene ComputingMilieux_MISCELLANEOUS Ecology Evolution Behavior and Systematics lcsh:SF1-1100 030304 developmental biology 0303 health sciences Research 0402 animal and dairy science 04 agricultural and veterinary sciences General Medicine 040201 dairy & animal science Hierarchical clustering Gene expression profiling [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics lcsh:Genetics Principal component analysis Animal Science and Zoology lcsh:Animal culture |
| Zdroj: | Genetics, Selection, Evolution : GSE Sørensen, P, Bonnet, A, Buitenhuis, B, Closset, R, Déjean, S, Delmas, C, Duval, M, Glass, E, Hedegaard, J, Hornshøj, H, Hulsegge, I, Jaffrézic, F, Jensen, K, Jiang, L, de Koning, D-J, Lê Cao, K-A, Nie, H, Petzl, W, Pool, M H, Robert-Granié, C, San Cristobal, M, Lund, M S, van Schothorst, E M, Schuberth, H-J, Seyfert, H-M, Tosser-Klopp, G, Waddington, D, Watson, M, Yang, W & Zerbe, H 2007, ' Analysis of the real EADGENE data set: Multivariate approaches and post analysis (Open Access publication) ', Genetics Selection Evolution, vol. 39, no. 6, pp. 651-668 . https://doi.org/10.1051/gse:2007030 Genetics Selection Evolution, Vol 39, Iss 6, Pp 651-668 (2007) HAL Genetics, selection, evolution, 39: 651 Genetics Selection Evolution Genetics Selection Evolution, BioMed Central, 2007, 39 (6), pp.651-668 |
| ISSN: | 1297-9686 0999-193X |
| DOI: | 10.1051/gse:2007030 |
| Popis: | The aim of this paper was to describe, and when possible compare, the multivariate methods used by the participants in the EADGENE WP1.4 workshop. The first approach was for class discovery and class prediction using evidence from the data at hand. Several teams used hierarchical clustering (HC) or principal component analysis (PCA) to identify groups of differentially expressed genes with a similar expression pattern over time points and infective agent (E. coli or S. aureus). The main result from these analyses was that HC and PCA were able to separate tissue samples taken at 24 h following E. coli infection from the other samples. The second approach identified groups of differentially co-expressed genes, by identifying clusters of genes highly correlated when animals were infected with E. coli but not correlated more than expected by chance when the infective pathogen was S. aureus. The third approach looked at differential expression of predefined gene sets. Gene sets were defined based on information retrieved from biological databases such as Gene Ontology. Based on these annotation sources the teams used either the GlobalTest or the Fisher exact test to identify differentially expressed gene sets. The main result from these analyses was that gene sets involved in immune defence responses were differentially expressed. |
| Databáze: | OpenAIRE |
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