WebaCGH: An interactive online tool for the analysis and display of array comparative genomic hybridisation data

Frankenberger, C; Wu X.; Gangi L.M.; Munroe D.J.; Harmon J.; Church D.; Urzua, U

Keywords: sequence, acid, system, dna, animals, expression, transcription, biology, program, gene, design, database, genome, hybridization, genomic, humans, chromosomes, array, computer, chromosome, article, languages, microarray, internet, oligonucleotide, software, genomics, analysis, online, genetic, graphics, profiling, DNA,, Complementary, comparative, Transcription,, programming, Computational, Nucleic, aided


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®. © 2006 Adis Data Information BV. All rights reserved.

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Título según SCOPUS: WebaCGH: An interactive online tool for the analysis and display of array comparative genomic hybridisation data
Título de la Revista: Applied Bioinformatics
Volumen: 5
Número: 2
Editorial: Adis Press
Fecha de publicación: 2006
Página de inicio: 125
Página final: 130
Idioma: eng
URL: http://www.scopus.com/inward/record.url?eid=2-s2.0-33744901128&partnerID=q2rCbXpz