DocumentCode :
844153
Title :
Autonomous system for web-based microarray image analysis
Author :
Bozinov, Daniel
Author_Institution :
Center for Human Molecular Genetics, Univ. of Nebraska Med. Center, Omaha, USA
Volume :
2
Issue :
4
fYear :
2003
Firstpage :
215
Lastpage :
220
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.
Keywords :
DNA; Internet; biological techniques; biology computing; feature extraction; genetics; molecular biophysics; DNA signals; Java-based interface; abstracted gene expression tables; algorithms; automated service; autonomous system; bioinformatics; gene expression values; gene spots; genome-wide medical diagnostics labs; grid parameters; iterative correction function; large-scale artifacts; metagrid parameters; microarray core facilities; raw image data; single microarray image; software-based feature extraction; superimposed grid templates; web-based microarray image analysis; DNA; Feature extraction; Gene expression; Humans; Image analysis; Java; Large-scale systems; Performance analysis; Signal analysis; Signal processing; Algorithms; Cluster Analysis; DNA; Gene Expression Profiling; Hypermedia; Image Enhancement; Image Interpretation, Computer-Assisted; Information Storage and Retrieval; Internet; Microscopy, Fluorescence; Nanotechnology; Oligonucleotide Array Sequence Analysis; Pattern Recognition, Automated; Reproducibility of Results; Robotics; Sensitivity and Specificity; Sequence Analysis, DNA; Software; User-Computer Interface;
fLanguage :
English
Journal_Title :
NanoBioscience, IEEE Transactions on
Publisher :
ieee
ISSN :
1536-1241
Type :
jour
DOI :
10.1109/TNB.2003.817021
Filename :
1254524
Link To Document :
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