Post-analyses of Microarray Data Publications

Following on from the success of the EADGENE Microarray Data Analysis Workshop (1-3 November 2006, Tune, Denmark), a joint EADGENE and SABRE working group on post-analyses of microarray data was set up. The aim of the working group was to evaluate and present already existing methods and software, and potentially to propose new methods to deal with the post-analyses of microarray data, using real data sourced from within EADGENE and SABRE.

The area of biology addressed by this workshop was gene expression studies in livestock looking at transcriptomic differences between treatments as well as genotypes and combinations of these. During a three-day workshop in November 2008, we discussed five aspects of these so-called post analyses of microarray data:

1. re-annotation of the probe set on DNA microarrays,
2. pathway analyses to identify significantly affected biological processes from microarray results,
3. reverse engineering of regulatory networks from microarray results,
4. the integration of gene expression studies with QTL detection studies and
5. the prediction of phenotypic outcomes using gene expression results.

The workshop organisers were Florence Jaffrezic (INRA), Jakob Hedegaard (University of Aarhus), Magali SanCristobal (INRA), Christophe Klopp (INRA) and Dirk-Jan de Koning (Roslin Institute and R(D)SVS, Edinburgh). The workshop was hosted by the Animal Sciences Group in Lelystad. For more information, please see the EADGENE or SABRE web sites.

The 14 papers arising from this working group are published together in BMC Proceedings 2009, Vol. 3 (Suppl. 4):

Introduction: The EADGENE and SABRE post-analyses workshop - Florence Jaffrezic, Jakob Hedegaard, Magali SanCristobal, Christophe Klopp, Dirk-Jan de Koning BMC Proceedings 2009, 3(Suppl 4):I1 (16 July 2009)  

Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis - Pieter BT Neerincx, Pierrot Casel, Dennis Prickett, Haisheng Nie, Michael Watson, Jack AM Leunissen, Martien AM Groenen, Christophe Klopp BMC Proceedings 2009, 3(Suppl 4):S1 (16 July 2009)

IMAD: flexible annotation of microarray sequences - Dennis Prickett, Michael Watson BMC Proceedings 2009, 3(Suppl 4):S2 (16 July 2009)  

sigReannot: an oligo-set re-annotation pipeline based on similarities with the Ensembl transcripts and Unigene clusters Pierrot Casel, Franccois Moreews, Sandrine Lagarrigue, Christophe Klopp BMC Proceedings 2009, 3(Suppl 4):S3 (16 July 2009)

OligoRAP - an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity - Pieter BT Neerincx, Han Rauwerda, Haisheng Nie, Martien AM Groenen, Timo M Breit, Jack AM Leunissen BMC Proceedings 2009, 3(Suppl 4):S4 (16 July 2009)  

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment - Jakob Hedegaard, Cristina Arce, Silvio Bicciato, Agnes Bonnet, Bart Buitenhuis, Melania Collado-Romero, Lene N Conley, Magali SanCristobal, Francesco Ferrari, Juan J Garrido, Martien AM Groenen, Henrik Hornshoj, Ina Hulsegge, Li Jiang, Angeles Jimenez-Marian, Arun Kommadath, Sandrine Lagarrigue, Jack AM Leunissen, Laurence Liaubet, Pieter BT Neerincx, Haisheng Nie, Jan van der Poel, Dennis Prickett, Maria Ramirez-Boo, Johanna MJ Rebel, Christle Robert-Granie, Axel Skarman, Mari A Smits, Peter Srensen, Gwenola Tosser-Klopp, Michael Watson BMC Proceedings 2009, 3(Suppl 4):S5 (16 July 2009)  

Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis - Angeles Jimnez-Marian, Melania Collado-Romero, Maria Ramirez-Boo, Cristina Arce, Juan J Garrido BMC Proceedings 2009, 3(Suppl 4):S6 (16 July 2009)

Use of GenMAPP and MAPPFinder to analyse pathways involved in chickens infected with the protozoan parasite Eimeria - Dennis Prickett, Michael Watson BMC Proceedings 2009, 3(Suppl 4):S7 (16 July 2009)  

Gene set analysis methods applied to chicken microarray expression data - Axel Skarman, Li Jiang, Hornshoj Henrik, Bart Buitenhuis, Jakob Hedegaard, Lene N Conley, Peter Srensen BMC Proceedings 2009, 3(Suppl 4):S8 (16 July 2009)  

Microarray data mining using Bioconductor packages - Haisheng Nie, Pieter BT Neerincx, Jan van der Poel, Francesco Ferrari, Silvio Bicciato, Jack AM Leunissen, Martien AM Groenen BMC Proceedings 2009, 3(Suppl 4):S9 (16 July 2009)

Globaltest and GOEAST: two different approaches for Gene Ontology analysis - Ina Hulsegge, Arun Kommadath, Mari A Smits BMC Proceedings 2009, 3(Suppl 4):S10 (16 July 2009)  

Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares - Agnes Bonnet, Sandrine Lagarrigue, Laurence Liaubet, Christele Robert-Granie, Magali SanCristobal, Gwenola Tosser-Klopp BMC Proceedings 2009, 3(Suppl 4):S11 (16 July 2009)

Gene network reconstruction from microarray data - Florence Jaffrezic, Gwenola Tosser-Klopp BMC Proceedings 2009, 3(Suppl 4):S12 (16 July 2009)

Predicting qualitative phenotypes from microarray data - the Eadgene pig data set - Christele Robert-Granie, Kim-Anh Le Cao, Magali SanCristobal BMC Proceedings 2009, 3(Suppl 4):S13 (16 July 2009)  

Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs - Vincent Jouffe, Suzanne Rowe, Laurence Liaubet, Bart Buitenhuis, Henrik Hornshoj, Magali SanCristobal, Pierre Mormede, DJ de Koning BMC Proceedings 2009, 3(Suppl 4):S14 (16 July 2009)