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NetR and AttR, Two New Bioinformatic Tools to Integrate Diverse Datasets into Cytoscape Network and Attribute Files

1
Department of Biology, California State University, Northridge (CSUN), CA 91330, USA
2
Department of Computer Science, California State University, Northridge (CSUN), CA 91330, USA
*
Author to whom correspondence should be addressed.
Genes 2019, 10(6), 423; https://doi.org/10.3390/genes10060423
Received: 16 April 2019 / Revised: 25 May 2019 / Accepted: 27 May 2019 / Published: 1 June 2019
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Abstract

High-throughput technologies have allowed researchers to obtain genome-wide data from a wide array of experimental model systems. 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. 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. 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. NetR also allows users to import protein and genetic interaction data from InterMine, which can further enrich a network model based on curated information. 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. View Full-Text
Keywords: genome-wide screens; genetic and protein interactions; biological networks; Cytoscape; Drosophila intestinal stem cells genome-wide screens; genetic and protein interactions; biological networks; Cytoscape; Drosophila intestinal stem cells
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Halajyan, A.; Weingart, N.; Yeahia, M.; Loza-Coll, M. NetR and AttR, Two New Bioinformatic Tools to Integrate Diverse Datasets into Cytoscape Network and Attribute Files. Genes 2019, 10, 423.

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