A Systematic, Data-driven Approach to the Combined Analysis of Microarray and QTL Data

C Rennie; H Hulme; P Fisher; L Hall; M Agaba; H A Noyes; S J Kemp; A Brass; M H Pinard; C Gay; P P Pastoret; B Dodet; European Anim Dis Biol Sci Res Council; Hlth Genom Network Excellence Anim; Inst Natl Rech Agron Food Safety; World Org Anim Hlth Int Assoc Biol

A Systematic, Data-driven Approach to the Combined Analysis of Microarray and QTL Data

C Rennie, H Hulme, P Fisher, L Hall, M Agaba, H A Noyes, S J Kemp, A Brass, M H Pinard (Editor), C Gay (Editor), P P Pastoret (Editor), B Dodet (Editor), European Anim Dis Biol Sci Res Council (Editor), Hlth Genom Network Excellence Anim (Editor), Inst Natl Rech Agron Food Safety (Editor), World Org Anim Hlth Int Assoc Biol (Editor)

Research output: Chapter in Book/Conference proceeding › Conference contribution

Abstract

High-throughput technologies inevitably produce vast quantities of data. This presents challenges in terms of developing effective analysis methods, particularly where the analysis involves combining data derived from different experimental technologies. In this investigation, a systematic approach was applied to combine microarray gene expression data, quantitative trait loci (QTL) data and pathway analysis resources in order to identify functional candidate genes underlying tolerance to Trypanosoma congolense infection in cattle. We automated much of the analysis using Taverna workflows previously developed for the study of trypanotolerance in the mouse model. Pathways represented by genes within the QTL regions were identified, and this list was subsequently ranked according to which pathways were over-represented in the set of genes that were differentially expressed (over time or between tolerant N'dama and susceptible Boran breeds) at various timepoints after T congolense infection. The genes within the QTL that played a role in the highest ranked pathways were flagged as good targets for further investigation and experimental confirmation.

Original language	English
Title of host publication	International Symposium on Animal Genomics for Animal Health
Editors	M H Pinard, C Gay, P P Pastoret, B Dodet, European Anim Dis Biol Sci Res Council, Hlth Genom Network Excellence Anim, Inst Natl Rech Agron Food Safety, World Org Anim Hlth Int Assoc Biol
Publisher	S. Karger AG
Pages	293-299
Number of pages	7
Volume	132
ISBN (Print)	1424-6074 978-3-8055-8619-1
Publication status	Published - 2007
Event	International Symposium on Animal Genomics for Animal Health - Paris, FRANCE Duration: 25 Oct 2007 → 27 Oct 2007

Conference

Conference	International Symposium on Animal Genomics for Animal Health
City	Paris, FRANCE
Period	25/10/07 → 27/10/07

Keywords

automated analysis
microarray
QTL
workflow
Biology
Biotechnology & Applied Microbiology

Cite this

Rennie, C., Hulme, H., Fisher, P., Hall, L., Agaba, M., Noyes, H. A., Kemp, S. J., Brass, A., Pinard, M. H. (Ed.), Gay, C. (Ed.), Pastoret, P. P. (Ed.), Dodet, B. (Ed.), Biol Sci Res Council, E. A. D. (Ed.), Genom Network Excellence Anim, H. (Ed.), Food Safety, I. N. R. A. (Ed.), & Int Assoc Biol, W. O. A. H. (Ed.) (2007). A Systematic, Data-driven Approach to the Combined Analysis of Microarray and QTL Data. In M. H. Pinard, C. Gay, P. P. Pastoret, B. Dodet, E. A. D. Biol Sci Res Council, H. Genom Network Excellence Anim, I. N. R. A. Food Safety, & W. O. A. H. Int Assoc Biol (Eds.), International Symposium on Animal Genomics for Animal Health (Vol. 132, pp. 293-299). S. Karger AG.

Rennie, C ; Hulme, H ; Fisher, P et al. / A Systematic, Data-driven Approach to the Combined Analysis of Microarray and QTL Data. International Symposium on Animal Genomics for Animal Health. editor / M H Pinard ; C Gay ; P P Pastoret ; B Dodet ; European Anim Dis Biol Sci Res Council ; Hlth Genom Network Excellence Anim ; Inst Natl Rech Agron Food Safety ; World Org Anim Hlth Int Assoc Biol. Vol. 132 S. Karger AG, 2007. pp. 293-299

@inproceedings{45773eb475b5453a8d03e712846528c0,

title = "A Systematic, Data-driven Approach to the Combined Analysis of Microarray and QTL Data",

abstract = "High-throughput technologies inevitably produce vast quantities of data. This presents challenges in terms of developing effective analysis methods, particularly where the analysis involves combining data derived from different experimental technologies. In this investigation, a systematic approach was applied to combine microarray gene expression data, quantitative trait loci (QTL) data and pathway analysis resources in order to identify functional candidate genes underlying tolerance to Trypanosoma congolense infection in cattle. We automated much of the analysis using Taverna workflows previously developed for the study of trypanotolerance in the mouse model. Pathways represented by genes within the QTL regions were identified, and this list was subsequently ranked according to which pathways were over-represented in the set of genes that were differentially expressed (over time or between tolerant N'dama and susceptible Boran breeds) at various timepoints after T congolense infection. The genes within the QTL that played a role in the highest ranked pathways were flagged as good targets for further investigation and experimental confirmation.",

keywords = "automated analysis, microarray, QTL, workflow, Biology, Biotechnology & Applied Microbiology",

author = "C Rennie and H Hulme and P Fisher and L Hall and M Agaba and Noyes, {H A} and Kemp, {S J} and A Brass and Pinard, {M H} and C Gay and Pastoret, {P P} and B Dodet and {Biol Sci Res Council}, {European Anim Dis} and {Genom Network Excellence Anim}, Hlth and {Food Safety}, {Inst Natl Rech Agron} and {Int Assoc Biol}, {World Org Anim Hlth}",

note = "Agr Res Serv, Biotechnol Rennie, C. Hulme, H. Fisher, P. Hall, L. Agaba, M. Noyes, H. A. Kemp, S. J. Brass, A. 7 BASEL BJA67; International Symposium on Animal Genomics for Animal Health ; Conference date: 25-10-2007 Through 27-10-2007",

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volume = "132",

pages = "293--299",

editor = "Pinard, {M H} and C Gay and Pastoret, {P P} and B Dodet and {Biol Sci Res Council}, {European Anim Dis} and {Genom Network Excellence Anim}, Hlth and {Food Safety}, {Inst Natl Rech Agron} and {Int Assoc Biol}, {World Org Anim Hlth}",

booktitle = "International Symposium on Animal Genomics for Animal Health",

publisher = "S. Karger AG",

address = "Switzerland",

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Rennie, C, Hulme, H, Fisher, P, Hall, L, Agaba, M, Noyes, HA, Kemp, SJ, Brass, A, Pinard, MH (ed.), Gay, C (ed.), Pastoret, PP (ed.), Dodet, B (ed.), Biol Sci Res Council, EAD (ed.), Genom Network Excellence Anim, H (ed.), Food Safety, INRA (ed.) & Int Assoc Biol, WOAH (ed.) 2007, A Systematic, Data-driven Approach to the Combined Analysis of Microarray and QTL Data. in MH Pinard, C Gay, PP Pastoret, B Dodet, EAD Biol Sci Res Council, H Genom Network Excellence Anim, INRA Food Safety & WOAH Int Assoc Biol (eds), International Symposium on Animal Genomics for Animal Health. vol. 132, S. Karger AG, pp. 293-299, International Symposium on Animal Genomics for Animal Health, Paris, FRANCE, 25/10/07.

A Systematic, Data-driven Approach to the Combined Analysis of Microarray and QTL Data. / Rennie, C; Hulme, H; Fisher, P et al.
International Symposium on Animal Genomics for Animal Health. ed. / M H Pinard; C Gay; P P Pastoret; B Dodet; European Anim Dis Biol Sci Res Council; Hlth Genom Network Excellence Anim; Inst Natl Rech Agron Food Safety; World Org Anim Hlth Int Assoc Biol. Vol. 132 S. Karger AG, 2007. p. 293-299.

Research output: Chapter in Book/Conference proceeding › Conference contribution

TY - GEN

T1 - A Systematic, Data-driven Approach to the Combined Analysis of Microarray and QTL Data

AU - Rennie, C

AU - Hulme, H

AU - Fisher, P

AU - Hall, L

AU - Agaba, M

AU - Noyes, H A

AU - Kemp, S J

AU - Brass, A

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A2 - Pastoret, P P

A2 - Dodet, B

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A2 - Gay, C

A2 - Pastoret, P P

A2 - Dodet, B

A2 - Biol Sci Res Council, European Anim Dis

A2 - Genom Network Excellence Anim, Hlth

A2 - Food Safety, Inst Natl Rech Agron

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N1 - Agr Res Serv, Biotechnol Rennie, C. Hulme, H. Fisher, P. Hall, L. Agaba, M. Noyes, H. A. Kemp, S. J. Brass, A. 7 BASEL BJA67

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N2 - High-throughput technologies inevitably produce vast quantities of data. This presents challenges in terms of developing effective analysis methods, particularly where the analysis involves combining data derived from different experimental technologies. In this investigation, a systematic approach was applied to combine microarray gene expression data, quantitative trait loci (QTL) data and pathway analysis resources in order to identify functional candidate genes underlying tolerance to Trypanosoma congolense infection in cattle. We automated much of the analysis using Taverna workflows previously developed for the study of trypanotolerance in the mouse model. Pathways represented by genes within the QTL regions were identified, and this list was subsequently ranked according to which pathways were over-represented in the set of genes that were differentially expressed (over time or between tolerant N'dama and susceptible Boran breeds) at various timepoints after T congolense infection. The genes within the QTL that played a role in the highest ranked pathways were flagged as good targets for further investigation and experimental confirmation.

AB - High-throughput technologies inevitably produce vast quantities of data. This presents challenges in terms of developing effective analysis methods, particularly where the analysis involves combining data derived from different experimental technologies. In this investigation, a systematic approach was applied to combine microarray gene expression data, quantitative trait loci (QTL) data and pathway analysis resources in order to identify functional candidate genes underlying tolerance to Trypanosoma congolense infection in cattle. We automated much of the analysis using Taverna workflows previously developed for the study of trypanotolerance in the mouse model. Pathways represented by genes within the QTL regions were identified, and this list was subsequently ranked according to which pathways were over-represented in the set of genes that were differentially expressed (over time or between tolerant N'dama and susceptible Boran breeds) at various timepoints after T congolense infection. The genes within the QTL that played a role in the highest ranked pathways were flagged as good targets for further investigation and experimental confirmation.

KW - automated analysis

KW - microarray

KW - QTL

KW - workflow

KW - Biology

KW - Biotechnology & Applied Microbiology

M3 - Conference contribution

SN - 1424-6074 978-3-8055-8619-1

VL - 132

SP - 293

EP - 299

BT - International Symposium on Animal Genomics for Animal Health

PB - S. Karger AG

T2 - International Symposium on Animal Genomics for Animal Health

Y2 - 25 October 2007 through 27 October 2007

ER -

Rennie C, Hulme H, Fisher P, Hall L, Agaba M, Noyes HA et al. A Systematic, Data-driven Approach to the Combined Analysis of Microarray and QTL Data. In Pinard MH, Gay C, Pastoret PP, Dodet B, Biol Sci Res Council EAD, Genom Network Excellence Anim H, Food Safety INRA, Int Assoc Biol WOAH, editors, International Symposium on Animal Genomics for Animal Health. Vol. 132. S. Karger AG. 2007. p. 293-299

A Systematic, Data-driven Approach to the Combined Analysis of Microarray and QTL Data

Abstract

Conference

Keywords

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