title: Autonomous system for Web-based microarray image analysis.
abstract: Software-based feature extraction from DNA microarray images still requires human intervention on various levels. Manual adjustment of grid and metagrid parameters, precise alignment of superimposed grid templates and gene spots, or simply identification of large-scale artifacts have to be performed beforehand to reliably analyze DNA signals and correctly quantify their expression values. Ideally, a Web-based system with input solely confined to a single microarray image and a data table as output containing measurements for all gene spots would directly transform raw image data into abstracted gene expression tables. Sophisticated algorithms with advanced procedures for iterative correction function can overcome imminent challenges in image processing. Herein is introduced an integrated software system with a Java-based interface on the client side that allows for decentralized access and furthermore enables the scientist to instantly employ the most updated software version at any given time. This software tool is extended from PixClust as used in Extractiff incorporated with Java Web Start deployment technology. Ultimately, this setup is destined for high-throughput pipelines in genome-wide medical diagnostics labs or microarray core facilities aimed at providing fully automated service to its users.
authors.affiliation: Center for Human Molecular Genetics, Munroe-Meyer Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA. dbozinov@unmc.edu
authors.forename: Daniel
authors.initials: D
authors.lastname: Bozinov
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D004247:DNA / Q000032:analysis* / Q000737:chemistry / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods; D019146:Hypermedia; D007089:Image Enhancement / Q000379:methods; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D016247:Information Storage and Retrieval; D020407:Internet; D008856:Microscopy, Fluorescence / Q000379:methods*; D036103:Nanotechnology / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated; D015203:Reproducibility of Results; D012371:Robotics / Q000379:methods*; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D014584:User-Computer Interface
chemical_list: D004247:DNA