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Journal of Integrative Bioinformatics

Editor-in-Chief: Schreiber, Falk / Hofestädt, Ralf

Managing Editor: Sommer, Björn

Ed. by Baumbach, Jan / Chen, Ming / Orlov, Yuriy / Allmer, Jens

Editorial Board: Giorgetti, Alejandro / Harrison, Andrew / Kochetov, Aleksey / Krüger, Jens / Ma, Qi / Matsuno, Hiroshi / Mitra, Chanchal K. / Pauling, Josch K. / Rawlings, Chris / Fdez-Riverola, Florentino / Romano, Paolo / Röttger, Richard / Shoshi, Alban / Soares, Siomar de Castro / Taubert, Jan / Tauch, Andreas / Yousef, Malik / Weise, Stephan / Hassani-Pak, Keywan


CiteScore 2017: 0.77

SCImago Journal Rank (SJR) 2017: 0.336

Open Access
Online
ISSN
1613-4516
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Volume 4, Issue 3

Issues

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

Sabah Khalid
  • Molecular Immunology Group, Microarray Facility, Division of BioSciences, Brunel University, Uxbridge, UB8 3PH, United Kingdom of Great Britain and Northern Ireland
  • Intelligent Data Analysis Group, Department of Information Systems and Computing,Brunel University, Uxbridge, UB8 3PH, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Mohsin Khan
  • Molecular Immunology Group, Microarray Facility, Division of BioSciences, Brunel University, Uxbridge, UB8 3PH, United Kingdom of Great Britain and Northern Ireland
  • Other articles by this author:
  • De Gruyter OnlineGoogle Scholar
/ Alistair Symonds
  • Immunology Group, Institute of Cell and Molecular Sciences, Barts and London School of Medicine, London, United Kingdom of Great Britain and Northern Ireland
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  • De Gruyter OnlineGoogle Scholar
/ Karl Fraser
  • Intelligent Data Analysis Group, Department of Information Systems and Computing, Brunel University, Uxbridge, UB8 3PH, United Kingdom of Great Britain and Northern Ireland
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  • De Gruyter OnlineGoogle Scholar
/ Ping Wang
  • Immunology Group, Institute of Cell and Molecular Sciences, Barts and London School of Medicine, London, United Kingdom of Great Britain and Northern Ireland
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/ Xiaohui Liu
  • Intelligent Data Analysis Group, Department of Information Systems and Computing, Brunel University, Uxbridge, UB8 3PH, United Kingdom of Great Britain and Northern Ireland
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/ Suling Li
  • Corresponding author
  • Molecular Immunology Group, Microarray Facility, Division of BioSciences, Brunel University, Uxbridge, UB8 3PH, United Kingdom of Great Britain and Northern Ireland
  • Email
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Published Online: 2016-10-18 | DOI: https://doi.org/10.1515/jib-2007-78

Abstract

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.

The software and database schema is freely available at ftp://ftp.brunel.ac.uk/cspgssk/CIDA/. Additional material is available online at http://www.brunel.ac.uk/about/acad/health/healthres/researchgroups/mi/publications/supplementary/cida

Keywords: microarrays; ontology; immunology; gene chip design; immune tolerance; data-fusion

About the article

Published Online: 2016-10-18

Published in Print: 2007-12-01


Citation Information: Journal of Integrative Bioinformatics, Volume 4, Issue 3, Pages 224–242, ISSN (Online) 1613-4516, DOI: https://doi.org/10.1515/jib-2007-78.

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© 2007 The Author(s). Published by Journal of Integrative Bioinformatics.. This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License. BY-NC-ND 4.0

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