The EADGENE and SABRE Post-analyses Workshop

Overview

Journal BMC Proc

Publisher Biomed Central

Specialty Biology

Date 2009 Jul 21

PMID 19615108

Authors

Florence Jaffrezic

Jakob Hedegaard

Magali SanCristobal

Christophe Klopp

Dirk-Jan de Koning

Affiliations

Soon will be listed here.

References

Hazard D, Liaubet L, SanCristobal M, Mormede P . Gene array and real time PCR analysis of the adrenal sensitivity to adrenocorticotropic hormone in pig. BMC Genomics. 2008; 9:101. PMC: 2289818. DOI: 10.1186/1471-2164-9-101. View

Jaffrezic F, Tosser-Klopp G . Gene network reconstruction from microarray data. BMC Proc. 2009; 3 Suppl 4:S12. PMC: 2712742. DOI: 10.1186/1753-6561-3-S4-S12. View

Sorensen P, Bonnet A, Buitenhuis B, Closset R, Dejean S, Delmas C . Analysis of the real EADGENE data set: multivariate approaches and post analysis (open access publication). Genet Sel Evol. 2007; 39(6):651-68. PMC: 2682812. DOI: 10.1186/1297-9686-39-6-651. View

de Koning D, Jaffrezic F, Lund M, Watson M, Channing C, Hulsegge I . The EADGENE Microarray Data Analysis Workshop (open access publication). Genet Sel Evol. 2007; 39(6):621-31. PMC: 2682810. DOI: 10.1186/1297-9686-39-6-621. View

Jouffe V, Rowe S, Liaubet L, Buitenhuis B, Hornshoj H, SanCristobal M . Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs. BMC Proc. 2009; 3 Suppl 4:S14. PMC: 2712744. DOI: 10.1186/1753-6561-3-S4-S14. View

Nie H, Neerincx P, van der Poel J, Ferrari F, Bicciato S, Leunissen J . Microarray data mining using Bioconductor packages. BMC Proc. 2009; 3 Suppl 4:S9. PMC: 2712752. DOI: 10.1186/1753-6561-3-S4-S9. View

Prickett D, Watson M . Use of GenMAPP and MAPPFinder to analyse pathways involved in chickens infected with the protozoan parasite Eimeria. BMC Proc. 2009; 3 Suppl 4:S7. PMC: 2712750. DOI: 10.1186/1753-6561-3-S4-S7. View

Hulsegge I, Kommadath A, Smits M . Globaltest and GOEAST: two different approaches for Gene Ontology analysis. BMC Proc. 2009; 3 Suppl 4:S10. PMC: 2712740. DOI: 10.1186/1753-6561-3-S4-S10. View

Bonnet A, Lagarrigue S, Liaubet L, Robert-Granie C, SanCristobal M, Tosser-Klopp G . Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares. BMC Proc. 2009; 3 Suppl 4:S11. PMC: 2712741. DOI: 10.1186/1753-6561-3-S4-S11. View

10.

Jimenez-Marin A, Collado-Romero M, Ramirez-Boo M, Arce C, Garrido J . Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis. BMC Proc. 2009; 3 Suppl 4:S6. PMC: 2712749. DOI: 10.1186/1753-6561-3-S4-S6. View

11.

Watson M, Perez-Alegre M, Baron M, Delmas C, Dovc P, Duval M . Analysis of a simulated microarray dataset: comparison of methods for data normalisation and detection of differential expression (open access publication). Genet Sel Evol. 2007; 39(6):669-83. PMC: 2682813. DOI: 10.1186/1297-9686-39-6-669. View

12.

Casel P, Moreews F, Lagarrigue S, Klopp C . sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters. BMC Proc. 2009; 3 Suppl 4:S3. PMC: 2712746. DOI: 10.1186/1753-6561-3-S4-S3. View

13.

Jaffrezic F, de Koning D, Boettcher P, Bonnet A, Buitenhuis B, Closset R . Analysis of the real EADGENE data set: comparison of methods and guidelines for data normalisation and selection of differentially expressed genes (open access publication). Genet Sel Evol. 2007; 39(6):633-50. PMC: 2682811. DOI: 10.1186/1297-9686-39-6-633. View

14.

Robert-Granie C, Le Cao K, SanCristobal M . Predicting qualitative phenotypes from microarray data - the Eadgene pig data set. BMC Proc. 2009; 3 Suppl 4:S13. PMC: 2712743. DOI: 10.1186/1753-6561-3-S4-S13. View

15.

Skarman A, Jiang L, Henrik H, Buitenhuis B, Hedegaard J, Conley L . Gene set analysis methods applied to chicken microarray expression data. BMC Proc. 2009; 3 Suppl 4:S8. PMC: 2712751. DOI: 10.1186/1753-6561-3-S4-S8. View

16.

Prickett D, Watson M . IMAD: flexible annotation of microarray sequences. BMC Proc. 2009; 3 Suppl 4:S2. PMC: 2712745. DOI: 10.1186/1753-6561-3-S4-S2. View

17.

Hedegaard J, Arce C, Bicciato S, Bonnet A, Buitenhuis B, Collado-Romero M . Methods for interpreting lists of affected genes obtained in a DNA microarray experiment. BMC Proc. 2009; 3 Suppl 4:S5. PMC: 2712748. DOI: 10.1186/1753-6561-3-s4-s5. View

18.

Desautes C, Bidanelt J, Milant D, Iannuccelli N, Amigues Y, Bourgeois F . Genetic linkage mapping of quantitative trait loci for behavioral and neuroendocrine stress response traits in pigs. J Anim Sci. 2002; 80(9):2276-85. DOI: 10.2527/2002.8092276x. View

19.

Neerincx P, Casel P, Prickett D, Nie H, Watson M, Leunissen J . Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis. BMC Proc. 2009; 3 Suppl 4:S1. PMC: 2712739. DOI: 10.1186/1753-6561-3-S4-S1. View

20.

Neerincx P, Rauwerda H, Nie H, Groenen M, Breit T, Leunissen J . OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity. BMC Proc. 2009; 3 Suppl 4:S4. PMC: 2712747. DOI: 10.1186/1753-6561-3-S4-S4. View