title: WebaCGH: an interactive online tool for the analysis and display of array comparative genomic hybridisation data.
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.
  
  
  BACKGROUND
  WebaCGH is freely accessible at http://129.43.22.27/WebaCGH/welcome.htm
  
  
  BACKGROUND
  Xiaolin Wu (forestwu@mail.nih.gov) or Ulises Urzúa (uurzua@med.uchile.cl).
authors.affiliation: Laboratory of Molecular Technology, Scientific Application International Corporation (SAIC) - Frederick, Inc., National Cancer Institute - Frederick, Frederick, Maryland, USA.
authors.forename: Casey
authors.initials: C
authors.lastname: Frankenberger
authors.forename: Xiaolin
authors.initials: X
authors.lastname: Wu
authors.forename: Jerry
authors.initials: J
authors.lastname: Harmon
authors.forename: Deanna
authors.initials: D
authors.lastname: Church
authors.forename: Lisa M
authors.initials: LM
authors.lastname: Gangi
authors.forename: David J
authors.initials: DJ
authors.lastname: Munroe
authors.forename: Ulises
authors.initials: U
authors.lastname: Urzúa
mesh_terms: D000818:Animals; D002875:Chromosomes / Q000648:ultrastructure; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D018076:DNA, Complementary / Q000378:metabolism; D020869:Gene Expression Profiling; D016678:Genome; D006801:Humans; D020407:Internet; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D011381:Programming Languages; D012984:Software; D014158:Transcription, Genetic
chemical_list: D018076:DNA, Complementary