Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

Jakob Hedegaard; Cristina Arce; Silvio Bicciato; Agnès Bonnet; Bart Buitenhuis; Melania Collado-Romero; Lene N Conley; Magali Sancristobal; Francesco Ferrari; Juan J Garrido; Martien A M Groenen; Henrik Hornshøj; Ina Hulsegge; Li Jiang; Angeles Jiménez-Marín; Arun Kommadath; Sandrine Lagarrigue; Jack A M Leunissen; Laurence Liaubet; Pieter B T Neerincx; Haisheng Nie; Jan van der Poel; Dennis Prickett; María Ramirez-Boo; Johanna M J Rebel; Christèle Robert-Granié; Axel Skarman; Mari A Smits; Peter Sørensen; Gwenola Tosser-Klopp; Michael Watson

doi:10.1186/1753-6561-3-S4-S5

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

Jakob Hedegaard, Cristina Arce, Silvio Bicciato, Agnès Bonnet, Bart Buitenhuis, Melania Collado-Romero, Lene N Conley, Magali Sancristobal, Francesco Ferrari, Juan J Garrido, Martien A M Groenen, Henrik Hornshøj, Ina Hulsegge, Li Jiang, Angeles Jiménez-Marín, Arun Kommadath, Sandrine Lagarrigue, Jack A M Leunissen, Laurence Liaubet, Pieter B T NeerincxHaisheng Nie, Jan van der Poel, Dennis Prickett, María Ramirez-Boo, Johanna M J Rebel, Christèle Robert-Granié, Axel Skarman, Mari A Smits, Peter Sørensen, Gwenola Tosser-Klopp, Michael Watson

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Abstract

The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria.

Original language	English
Pages (from-to)	S5
Journal	BMC Proceedings
Volume	3
Issue number	Suppl 4
DOIs	https://doi.org/10.1186/1753-6561-3-S4-S5
Publication status	Published - 2009
Event	EADGENE and SABRE Post-analyses Workshop - Lelystad, Netherlands Duration: 12 Nov 2008 → 14 Nov 2008

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10.1186/1753-6561-3-S4-S5

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment
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http://www.biomedcentral.com/1753-6561/3/S4/S5/abstract

Ark Genomics
Watson, M., Archibald, A. & Burt, D.
BBSRC
1/04/12 → 31/03/17
Project: Research

Cite this

Hedegaard, J., Arce, C., Bicciato, S., Bonnet, A., Buitenhuis, B., Collado-Romero, M., Conley, L. N., Sancristobal, M., Ferrari, F., Garrido, J. J., Groenen, M. A. M., Hornshøj, H., Hulsegge, I., Jiang, L., Jiménez-Marín, A., Kommadath, A., Lagarrigue, S., Leunissen, J. A. M., Liaubet, L., ... Watson, M. (2009). Methods for interpreting lists of affected genes obtained in a DNA microarray experiment. BMC Proceedings, 3 (Suppl 4), S5. https://doi.org/10.1186/1753-6561-3-S4-S5

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abstract = "The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria.",

author = "Jakob Hedegaard and Cristina Arce and Silvio Bicciato and Agn{\`e}s Bonnet and Bart Buitenhuis and Melania Collado-Romero and Conley, {Lene N} and Magali Sancristobal and Francesco Ferrari and Garrido, {Juan J} and Groenen, {Martien A M} and Henrik Hornsh{\o}j and Ina Hulsegge and Li Jiang and Angeles Jim{\'e}nez-Mar{\'i}n and Arun Kommadath and Sandrine Lagarrigue and Leunissen, {Jack A M} and Laurence Liaubet and Neerincx, {Pieter B T} and Haisheng Nie and {van der Poel}, Jan and Dennis Prickett and Mar{\'i}a Ramirez-Boo and Rebel, {Johanna M J} and Christ{\`e}le Robert-Grani{\'e} and Axel Skarman and Smits, {Mari A} and Peter S{\o}rensen and Gwenola Tosser-Klopp and Michael Watson",

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doi = "10.1186/1753-6561-3-S4-S5",

language = "English",

volume = "3 ",

pages = "S5",

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Hedegaard, J, Arce, C, Bicciato, S, Bonnet, A, Buitenhuis, B, Collado-Romero, M, Conley, LN, Sancristobal, M, Ferrari, F, Garrido, JJ, Groenen, MAM, Hornshøj, H, Hulsegge, I, Jiang, L, Jiménez-Marín, A, Kommadath, A, Lagarrigue, S, Leunissen, JAM, Liaubet, L, Neerincx, PBT, Nie, H, van der Poel, J, Prickett, D, Ramirez-Boo, M, Rebel, JMJ, Robert-Granié, C, Skarman, A, Smits, MA, Sørensen, P, Tosser-Klopp, G & Watson, M 2009, 'Methods for interpreting lists of affected genes obtained in a DNA microarray experiment', BMC Proceedings, vol. 3 , no. Suppl 4, pp. S5. https://doi.org/10.1186/1753-6561-3-S4-S5

TY - JOUR

T1 - Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

AU - Hedegaard, Jakob

AU - Arce, Cristina

AU - Bicciato, Silvio

AU - Bonnet, Agnès

AU - Buitenhuis, Bart

AU - Collado-Romero, Melania

AU - Conley, Lene N

AU - Sancristobal, Magali

AU - Ferrari, Francesco

AU - Garrido, Juan J

AU - Groenen, Martien A M

AU - Hornshøj, Henrik

AU - Hulsegge, Ina

AU - Jiang, Li

AU - Jiménez-Marín, Angeles

AU - Kommadath, Arun

AU - Lagarrigue, Sandrine

AU - Leunissen, Jack A M

AU - Liaubet, Laurence

AU - Neerincx, Pieter B T

AU - Nie, Haisheng

AU - van der Poel, Jan

AU - Prickett, Dennis

AU - Ramirez-Boo, María

AU - Rebel, Johanna M J

AU - Robert-Granié, Christèle

AU - Skarman, Axel

AU - Smits, Mari A

AU - Sørensen, Peter

AU - Tosser-Klopp, Gwenola

AU - Watson, Michael

PY - 2009

Y1 - 2009

N2 - The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria.

AB - The aim of this paper was to describe and compare the methods used and the results obtained by the participants in a joint EADGENE (European Animal Disease Genomic Network of Excellence) and SABRE (Cutting Edge Genomics for Sustainable Animal Breeding) workshop focusing on post analysis of microarray data. The participating groups were provided with identical lists of microarray probes, including test statistics for three different contrasts, and the normalised log-ratios for each array, to be used as the starting point for interpreting the affected probes. The data originated from a microarray experiment conducted to study the host reactions in broilers occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria.

U2 - 10.1186/1753-6561-3-S4-S5

DO - 10.1186/1753-6561-3-S4-S5

M3 - Article

C2 - 19615118

VL - 3

SP - S5

JO - BMC Proceedings

JF - BMC Proceedings

IS - Suppl 4

T2 - EADGENE and SABRE Post-analyses Workshop

Y2 - 12 November 2008 through 14 November 2008

ER -

Methods for interpreting lists of affected genes obtained in a DNA microarray experiment

Abstract

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