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This wealth of data is usually uploaded in their raw format to public repositories, such as the Gene Expression Omnibus (GEO) Database ( ), the European Bioinformatics Institute (EMBL-EBI) ( ), the DNA Data Bank of Japan (DDBJ) ( ) and others, and can later be queried in a series of downstream applications and metanalyses by colleagues worldwide. Recent technological advances have allowed researchers to produce a large amount of genomic and transcriptomic data in a wide range of experimental systems. We expect that NetR/AttR will allow experimental biologists to mine a largely unexploited wealth of data in their fields and facilitate their integration into hypothetical models to be tested experimentally. NetR also allows users to import protein and genetic interaction data from InterMine, which can further enrich a network model based on curated information.
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We have developed two programs (NetR and AttR), which allow experimental biologists with little to no programming background to integrate publicly available datasets into files that can be later visualized with Cytoscape to display hypothetical networks that result from combining individual datasets, as well as a series of published attributes related to the genes or proteins in the network. The reasons behind such data underutilization include a widespread lack of programming expertise among experimentalist biologists to carry out the necessary file reformatting that is often necessary to integrate published data from disparate sources. Unfortunately, however, new data generation tends to significantly outpace data re-utilization, and most high throughput datasets are only rarely used in subsequent studies or to generate new hypotheses to be tested experimentally.
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High-throughput technologies have allowed researchers to obtain genome-wide data from a wide array of experimental model systems.