Analysis of the real EADGENE data set: Multivariate approaches and post analysis (Open Access publication)

Genetics Selection Evolution

Volumn 39, Issue 6, 2007, Pages 651-668

  Sørensen, Peter ^a   Bonnet, Agnès ^b   Buitenhuis, Bart ^a   Closset, Rodrigue ^c   Déjean, Sébastien ^d   Delmas, Céline ^b   Duval, Mylène ^b   Glass, Liz ^e   Hedegaard, Jakob ^a   Hornshøj, Henrik ^a   Hulsegge, Ina ^f   Jaffrézic, Florence ^b   Jensen, Kirsty ^e   Jiang, Li ^a   De Koning, Dirk Jan ^e   Lê Cao, Kim Anh ^b,d   Nie, Haisheng ^f   Petzl, Wolfram ^g   Pool, Marco H ^f   Robert Granié, Christèle ^b   San Cristobal, Magali ^b   Lund, Mogens Sandø ^a   Van Schothorst, Evert M ^f   Schuberth, Hans Joachim ^h   Seyfert, Hans Martin ⁱ   Tosser Klopp, Gwenola ^b   Waddington, David ^e   Watson, Michael ^j   Yang, Wei ⁱ   Zerbe, Holm ^g   more..

^a DANISH INSTITUTE OF AGRICULTURAL SCIENCES   (Denmark)

^b CEMAGREF   (France)

^c UNIVERSITY OF LIÈGE   (Belgium)

^d INSTITUT DE MATHÉMATIQUES DE TOULOUSE   (France)

^e UNIVERSITY OF EDINBURGH   (United Kingdom)

^f WAGENINGEN UNIVERSITY   (Netherlands)

^g UNIVERSITY OF MUNICH   (Germany)

^h UNIVERSITY OF VETERINARY MEDICINE HANNOVER   (Germany)

ⁱ LEIBNIZ INSTITUTE FOR FARM ANIMAL BIOLOGY FBN   (Germany)

^j INSTITUTE FOR ANIMAL HEALTH   (United Kingdom)

more..

Author keywords

Bovine annotation; Bovine microarray; Gene set analysis; Mastitis; Multivariate approaches

Indexed keywords

BACTERIAL DISEASE; CATTLE; CLUSTER ANALYSIS; DATA INTERPRETATION; DATA SET; GENE EXPRESSION; INFECTIOUS DISEASE; MULTIVARIATE ANALYSIS; PRINCIPAL COMPONENT ANALYSIS;

ANIMAL; ANIMAL DISEASE; ARTICLE; CATTLE; CATTLE DISEASE; COMPARATIVE STUDY; DNA MICROARRAY; DOMESTIC ANIMAL; ENTEROBACTER INFECTION; EUROPE; FEMALE; GENE EXPRESSION PROFILING; GENETIC DATABASE; GENETICS; HOST PATHOGEN INTERACTION; MULTIVARIATE ANALYSIS; STAPHYLOCOCCUS INFECTION; STATISTICAL ANALYSIS; STATISTICS;

ANIMALS; ANIMALS, DOMESTIC; CATTLE; DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; ESCHERICHIA COLI INFECTIONS; EUROPE; FEMALE; GENE EXPRESSION PROFILING; HOST-PATHOGEN INTERACTIONS; MASTITIS, BOVINE; MULTIVARIATE ANALYSIS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; STAPHYLOCOCCAL INFECTIONS;

ANIMALIA; BOVINAE; ESCHERICHIA COLI; STAPHYLOCOCCUS AUREUS;

EID: 36849079353     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1051/gse:2007030     Document Type: Article

References (20)

1. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G., Gene ontology: tool for the unification of biology, The Gene Ontology Consortium, Nat. Genet. 25 (2000) 25-29.
2. Bannerman D.D., Paape M.J., Lee J.W., Zhao X., Hope J.C., Rainard P., Escherichia coli and Staphylococcus aureus elicit differential innate immune responses following intramammary infection, Clin. Diagn. Lab Immunol. 11 (2004) 463-472.
3. Breiman L., Random forests, Mach Learn 45 (2001) 5-32.
4. Breiman L., Friedman J., Stone C.J., Olshen R.A., Classification and regression trees, Chapman & Hall, New York, 1984.
5. de Koning D.J., Jaffrézic F., Lund M.S., Watson M., Channing C., Hulsegge I., Pool H.M., Buitenhuis B., Hedegaard J., Hornshøj H., Jiang L., Sørensen P., Marot G., Delmas C., Lê Cao K.-A., San Cristobal M., Baron M.D., Malinverni R., Stella A., Brunner R.M., Seyfert H.-M., Jensen K., Mouzaki D., Waddington D., Jiménez-Marín Á., Pérez-Alegre M., Pérez-Reinado E., Closset R., Detilleux J.C., Dovč P., Lavrič M., Nie H., Janss L., The EADGENE Microarray Data Analysis Workshop, Genet. Sel. Evol. 39 (2007) 621-631.
6. Déjean S., Martin P., Baccini A., Besse P., Clustering time series gene expression data using smoothing spline derivativesEURASIP, J. Bioinform. Syst. Biol., vol. 2007, article ID 70561, 10 pages.
7. Draghici S., Khatri P., Martins R.P., Ostermeier G.C., Krawetz S.A., Global functional profiling of gene expression, Genomics 81 (2003) 98-104.
8. Durinck S., Moreau Y., Kasprzyk A., Davis S., De M.B., Brazma A., Huber W., BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis, Bioinformatics 21 (2005) 3439-3440.
9. Eisen M.B., Spellman P.T., Brown P.O., Botstein D., Cluster analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci. USA 95 (1998) 14863-14868.
10. Falcon S., Gentleman R., Using GOstats to test gene lists for GO term association, Bioinformatics 23 (2007) 257-258.
11. Gadat S., Younes L., A stochastic algorithm for feature selection in pattern recognition, J. Mach. Learn. 8 (2007) http://jmlr.csail.mit.edu/papers/ v8/.
12. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y., Zhang J., Bioconductor: open software development for computational biology and bioinformatics, Genome Biol. 5 (2004) R80.
13. Goeman J.J., Buhlmann P., Analyzing gene expression data in terms of gene sets: methodological issues, Bioinformatics 23 (2007) 980-987.
14. Goeman J.J., Oosting J., Cleton-Jansen A.M., Anninga J.K., van Houwelingen H.C., Testing association of a pathway with survival using gene expression data, Bioinformatics 21 (2005) 1950-1957.
15. Jaffrézic F., de Koning D.J., Boettcher P.J., Bonnet A., Buitenhuis B., Closset R., Déjean S., Delmas C., Detilleux J.C., Dovč P., Duval M., Foulley J.-L., Hedegaard J., Hornshoj H., Hulsegge I., Janss L., Jensen K., Jiang L., Lavrič M., Lê Cao K.-A., Lund M.S., Malinverni R., Marot G., Nie H., Petzl W., Pool H.M., Robert-Granié C., San Cristobal M., van Schotshorst E.M., Schuberth H.-J., Sørensen P., Stella A., Tosser-Klopp G., Waddington D., Watson M., Yang W., Zerbe H., Seyfert H.-M., Analysis of the real EADGENE data set: Comparison of methods and guidelines for data normalisation and selection of differentially expressed genes, Genet. Sel. Evol. 39 (2007) 633-650.
16. Lê Cao K.A., Bonnet A., Besse P., Robert-Granié C., San Cristobal M., Feature selection with random forests for unbalanced multiclass microarray data: application in pig ovarian follicular development, Belo Horizonte, Brazil, 13 August 2006, Proceedings of the 8th World Congress on Genetics Applied to Livestock Production.
17. Robert-Granié C., Baccini A., Besse P., Déjean S., Ferré P.J., Liaubet L., Martin P.G.P., San Cristobal M., Kinetics analysis of microarray data using semiparametric mixed models, Belo Horizonte, Brazil, 13 August 2006, Proceedings of the 8th World Congress on Genetics Applied to Livestock Production.
18. Vangroenweghe F., Rainard P., Paape M., Duchateau L., Burvenich C., Increase of Escherichia coli inoculum doses induces faster innate immune response in primiparous cows, J. Dairy Sci. 87 (2004) 4132-4144.
19. Watson M., CoXpress: differential co-expression in gene expression data, BMC Bioinformatics 7 (2006) 509.
20. Zhang J., Carey V., Gentleman R., An extensible application for assembling annotation for genomic data, Bioinformatics 19 (2003) 155-156.