CIDA: An integrated software for the design, characterisation and global comparison of microarrays

Microarray technology has had a significant impact in the field of systems biology involving the investigation into the biological systems that regulate human life. Identifying genes of significant interest within any given disease on an individual basis is no doubt time consuming and inefficient wh...

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Main Authors: Khalid Sabah, Khan Mohsin, Symonds Alistair, Fraser Karl, Wang Ping, Liu Xiaohui, Li Suling
Format: Article
Language:English
Published: De Gruyter 2007-12-01
Series:Journal of Integrative Bioinformatics
Subjects:
Online Access:https://doi.org/10.1515/jib-2007-78
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spelling doaj-dca74b22a4934b739c3d5afeb71189f32021-09-06T19:40:30ZengDe GruyterJournal of Integrative Bioinformatics1613-45162007-12-014322424210.1515/jib-2007-78biecoll-jib-2007-78CIDA: An integrated software for the design, characterisation and global comparison of microarraysKhalid Sabah0Khan Mohsin1Symonds Alistair2Fraser Karl3Wang Ping4Liu Xiaohui5Li Suling6Molecular Immunology Group, Microarray Facility, Division of BioSciences, Brunel University, Uxbridge, UB8 3PH, United Kingdom of Great Britain and Northern IrelandMolecular Immunology Group, Microarray Facility, Division of BioSciences, Brunel University, Uxbridge, UB8 3PH, United Kingdom of Great Britain and Northern IrelandImmunology Group, Institute of Cell and Molecular Sciences, Barts and London School of Medicine, London, United Kingdom of Great Britain and Northern IrelandIntelligent Data Analysis Group, Department of Information Systems and Computing, Brunel University, Uxbridge, UB8 3PH, United Kingdom of Great Britain and Northern IrelandImmunology Group, Institute of Cell and Molecular Sciences, Barts and London School of Medicine, London, United Kingdom of Great Britain and Northern IrelandIntelligent Data Analysis Group, Department of Information Systems and Computing, Brunel University, Uxbridge, UB8 3PH, United Kingdom of Great Britain and Northern IrelandMolecular Immunology Group, Microarray Facility, Division of BioSciences, Brunel University, Uxbridge, UB8 3PH, United Kingdom of Great Britain and Northern IrelandMicroarray technology has had a significant impact in the field of systems biology involving the investigation into the biological systems that regulate human life. Identifying genes of significant interest within any given disease on an individual basis is no doubt time consuming and inefficient when considering the complexity of the human genome. Thus, the genetic profiling of the entire human genome in a single experiment has resulted in microarray technology becoming a widely used experimental tool. However, without the use of tools for several aspects of microarray data analysis the technology is limited. To date, no such tool has been developed that allows the integration of numerous microarray results from different research laboratories as well as the design of customised gene chips in a cost-effective manner. In light of this, we have designed the first integrated and automated software called Chip Integration, Design and Annotation (CIDA) for the cross comparison, design and functional annotation of microarray gene chips. The software provides molecular biologists with the control to cross compare the biological signatures generated from multiple microarray studies, design custom microarray gene chips based on their research requirements and lastly characterise microarray data in the context of immunogenomics. Through the relative comparison of related microarray experiments we have identified 258 genes with common gene expression profiles that are not only upregulated in anergic T cells, but also in cells over-expressing the transcription factor Egr2, that has been identified to play a role in T cell anergy. Using the gene chip design aspect of CIDA we have designed and subsequently fabricate immuno-tolerance gene chips consisting of 1758 genes for further research.https://doi.org/10.1515/jib-2007-78microarraysontologyimmunologygene chip designimmune tolerancedata-fusion
collection DOAJ
language English
format Article
sources DOAJ
author Khalid Sabah
Khan Mohsin
Symonds Alistair
Fraser Karl
Wang Ping
Liu Xiaohui
Li Suling
spellingShingle Khalid Sabah
Khan Mohsin
Symonds Alistair
Fraser Karl
Wang Ping
Liu Xiaohui
Li Suling
CIDA: An integrated software for the design, characterisation and global comparison of microarrays
Journal of Integrative Bioinformatics
microarrays
ontology
immunology
gene chip design
immune tolerance
data-fusion
author_facet Khalid Sabah
Khan Mohsin
Symonds Alistair
Fraser Karl
Wang Ping
Liu Xiaohui
Li Suling
author_sort Khalid Sabah
title CIDA: An integrated software for the design, characterisation and global comparison of microarrays
title_short CIDA: An integrated software for the design, characterisation and global comparison of microarrays
title_full CIDA: An integrated software for the design, characterisation and global comparison of microarrays
title_fullStr CIDA: An integrated software for the design, characterisation and global comparison of microarrays
title_full_unstemmed CIDA: An integrated software for the design, characterisation and global comparison of microarrays
title_sort cida: an integrated software for the design, characterisation and global comparison of microarrays
publisher De Gruyter
series Journal of Integrative Bioinformatics
issn 1613-4516
publishDate 2007-12-01
description Microarray technology has had a significant impact in the field of systems biology involving the investigation into the biological systems that regulate human life. Identifying genes of significant interest within any given disease on an individual basis is no doubt time consuming and inefficient when considering the complexity of the human genome. Thus, the genetic profiling of the entire human genome in a single experiment has resulted in microarray technology becoming a widely used experimental tool. However, without the use of tools for several aspects of microarray data analysis the technology is limited. To date, no such tool has been developed that allows the integration of numerous microarray results from different research laboratories as well as the design of customised gene chips in a cost-effective manner. In light of this, we have designed the first integrated and automated software called Chip Integration, Design and Annotation (CIDA) for the cross comparison, design and functional annotation of microarray gene chips. The software provides molecular biologists with the control to cross compare the biological signatures generated from multiple microarray studies, design custom microarray gene chips based on their research requirements and lastly characterise microarray data in the context of immunogenomics. Through the relative comparison of related microarray experiments we have identified 258 genes with common gene expression profiles that are not only upregulated in anergic T cells, but also in cells over-expressing the transcription factor Egr2, that has been identified to play a role in T cell anergy. Using the gene chip design aspect of CIDA we have designed and subsequently fabricate immuno-tolerance gene chips consisting of 1758 genes for further research.
topic microarrays
ontology
immunology
gene chip design
immune tolerance
data-fusion
url https://doi.org/10.1515/jib-2007-78
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