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WebaCGH

An Interactive Online Tool for the Analysis and Display of Array Comparative Genomic Hybridisation Data

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  • Published:
Applied Bioinformatics

Abstract

Gene copy number variations occur both in normal cells and in numerous pathologies including cancer and developmental diseases. Array comparative genomic hybridisation (aCGH) is an emerging technology that allows detection of chromosomal gains and losses in a high-resolution format. When aCGH is performed on cDNA and oligonucleotide microarrays, the impact of DNA copy number on gene transcription profiles may be directly compared. We have created an online software tool, WebaCGH, that functions to (i) upload aCGH and gene transcription results from multiple experiments; (ii) identify significant aberrant regions using a local Z-score threshold in user-selected chromosomal segments subjected to smoothing with moving averages; and (iii) display results in a graphical format with full genome and individual chromosome views. In the individual chromosome display, data can be zoomed in/out in both dimensions (i.e. ratio and physical location) and plotted features can have ‘mouse over’ linking to outside databases to identify loci of interest. Uploaded data can be stored indefinitely for subsequent retrieval and analysis. WebaCGH was created as a Java™-based web application using the open-source database MySQL®.

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Acknowledgements

This article is dedicated to the memory of José Urzúa. We thank Seymour Davies and John Powell for help in data management. Dr Urzúa was an Exchange Scientist at the Laboratory of Molecular Technology supported by a fellowship from the Oncology Research Faculty Development Program, Office of International Affairs of the National Cancer Institute. This work has been funded in whole or in part with federal funds from the National Cancer Institute, National Institutes of Health under contract no. N01-C0-12400.

The authors declare no conflicts of interest regarding the contents of this manuscript.

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Authors and Affiliations

  1. Laboratory of Molecular Technology, Scientific Application International Corporation (SAIC) - Frederick, Inc., National Cancer Institute - Frederick, Frederick, Maryland, USA

    Casey Frankenberger, Xiaolin Wu, Lisa M. Gangi & David J. Munroe

  2. Scientific Application International Corporation (SAIC), Annapolis, Maryland, USA

    Jerry Harmon

  3. National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA

    Deanna Church

  4. Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Avda. Independencia #1027, Santiago, Chile

    Ulises Urzúa

Authors
  1. Casey Frankenberger
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  2. Xiaolin Wu
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  3. Jerry Harmon
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  4. Deanna Church
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  5. Lisa M. Gangi
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  6. David J. Munroe
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  7. Ulises Urzúa
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Corresponding author

Correspondence to Ulises Urzúa.

Additional information

Availability: WebaCGH is freely accessible at http://129.43.22.27/WebaCGH/welcome.htm

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Frankenberger, C., Wu, X., Harmon, J. et al. WebaCGH. Appl-Bioinformatics 5, 125–130 (2006). https://doi.org/10.2165/00822942-200605020-00009

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  • DOI: https://doi.org/10.2165/00822942-200605020-00009

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