1,721,029 research outputs found
Gene Array Analyzer Software: a multi-user platform for management, analysis and visualization of gene expression data from replicate experiments
No full textBackground. Availability of gene sequences identified by many genome projects and improvements of nanotechnology have made high-throughput experiments a powerful tool to study the differential expression of thousands of genes at once. Nevertheless, these experiments produce a huge amount of data presenting variability of gene expression levels and noise. An adequate software framework is therefore required to manage and analyze these data in order to mine new biological information. Design and implementation of the Gene Array Analyzer Software (GAAS), a new application providing efficient management and appropriate analysis of a great quantity of gene expression data from replicate experiments, is described.
Methods. In a multi-user environment a database based management system provides flexibility in handling data from distinct high-throughput technologies and custom data output formats. Analysis algorithms allow background and spot quality evaluation, data normalization, and assessment of statistical significance of gene differential expressions also from replicate experiments.
Results. The developed GAAS application, composed of management, analysis, and visualization frameworks, enables each user to perform parametric gene differential expression analyses and to store in output databases analysis parameter used and obtained results. An intuitive user interface enables interactive browsing of expression profiles and analysis results, providing visualization of identified candidate regulated gene data both in tabular and graphical form.
Conclusions. GAAS is a powerful software framework for flexible management and fast automatic suitable analyses of gene expression data across multiple replica experiments. It is freely available for downloading for academic and non-profit use at http://www.medinfopoli.polimi.it/GAAS/
A database-based application for management and statistical analysis of high-throughput gene expression data
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MyWEST: My Web Extraction Software Tool for effective mining of annotations from web-based databanks
No full textMotivation: High-throughput technologies create the necessity to mine large amounts of gene annotations from diverse databanks, and to integrate the resulting data. Most databanks can be interrogated only via Web, for a single gene at a time, and query results are generally available only in the HTML format. Although some databanks provide batch retrieval of data via FTP, this requires expertise and resources for locally reimplementing the databank.
Results: We developed MyWEST, a tool aimed at researchers without extensive informatics skills or resources, which exploits user-defined templates to easily mine selected annotations from different Web-interfaced databanks, and aggregates and structures results in an automatically updated database. Using microarray results from a model system of retinoic acid-induced differentiation, MyWEST effectively gathered relevant annotations from various biomolecular databanks, highlighted significant biological characteristics and supported a global approach to the understanding of complex cellular mechanisms.
Availability: MyWEST is freely available for non-profit use at http://www.medinfopoli.polimi.it/MyWEST/
Contact: [email protected]
GeneWebEx: Gene annotation Web Extraction, aggregation, and updating from web-interfaced biomolecular databanks
No full textNumerous genomic annotations are currently stored in different Web-accessible databanks that scientists need to mine with user-defined queries and in a batch mode to orderly integrate the diverse extracted data in suitable user-customizable working environments. Unfortunately, to date, most accessible databanks can be interrogated only for a single gene or protein at a time and generally the data retrieved are available in HTML page format only. We developed GeneWebEx to effectively mine data of interest in different HTML pages of Web-interfaced databanks, and organize extracted data for further analyses. GeneWebEx utilizes user-defined templates to identify data to extract, and aggregates and structures them in a database designed to allocate the various extractions from distinct biomolecular databanks. Moreover, a template-based module enables automatic updating of extracted data. Validations performed on GeneWebEx allowed us to efficiently gather relevant annotations from various sources, and comprehensively query them to highlight significant biological characteristics
GeneWebEx: Gene annotation Web Extraction, aggregation, and updating from web biomolecular databanks
No full textSoftware agents for extracting, aggregating and updating data from web pages of genomic databanks
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