Authors: Frankenberger, Casey¹; Wu, Xiaolin¹; Harmon, Jerry²; Church, Deanna³; Gangi, Lisa M.¹; Munroe, David J.¹; Urzúa, Ulises⁴

Source: Applied Bioinformatics, Volume 5, Number 2, 2006 , pp. 125-130(6)

Publisher: Adis International

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^®.

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

Contact: Xiaolin Wu (forestwu@mail.nih.gov) or Ulises Urzúa (uurzua@med.uchile.cl)

Keywords: Bioinformatics; Computers

Document Type: Research article

Affiliations: 1: 1 Laboratory of Molecular Technology, Scientific Application International Corporation (SAIC) – Frederick, Inc., National Cancer Institute – Frederick, Frederick, Maryland, USA 2: 2 Scientific Application International Corporation (SAIC), Annapolis, Maryland, USA 3: 3 National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland, USA 4: 4 Programa de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile

Publication date: 2006-01-01

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• In this Subject: Biology ,  Computer Science ,  Mathematics and Statistics
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