Dataset Information

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

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.

SUBMITTER: Halajyan A

PROVIDER: S-EPMC6628208 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature

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

Halajyan Armen A Weingart Natalie N Yeahia Mirza M Loza-Coll Mariano M

Genes 20190601 6

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 ...[more]

PMID: 31159440

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Project description:IntroductionThe high complexity and dynamic nature of the regulation of gene expression, protein synthesis, and protein activity pose a challenge to fully understand the cellular machinery. By deciphering the role of important players, including transcription factors, microRNAs, or small molecules, a better understanding of key regulatory processes can be obtained. Various databases contain information on the interactions of regulators with their targets for different organisms, data recently being extended with the results of the ENCODE (Encyclopedia of DNA Elements) project. A systems biology approach integrating our understanding on different regulators is essential in interpreting the regulation of molecular biological processes.ImplementationWe developed CyTargetLinker (http://projects.bigcat.unimaas.nl/cytargetlinker), a Cytoscape app, for integrating regulatory interactions in network analysis. Recently we released CyTargetLinker as one of the first apps for Cytoscape 3. It provides a user-friendly and flexible interface to extend biological networks with regulatory interactions, such as microRNA-target, transcription factor-target and/or drug-target. Importantly, CyTargetLinker employs identifier mapping to combine various interaction data resources that use different types of identifiers.ResultsThree case studies demonstrate the strength and broad applicability of CyTargetLinker, (i) extending a mouse molecular interaction network, containing genes linked to diabetes mellitus, with validated and predicted microRNAs, (ii) enriching a molecular interaction network, containing DNA repair genes, with ENCODE transcription factor and (iii) building a regulatory meta-network in which a biological process is extended with information on transcription factor, microRNA and drug regulation.ConclusionsCyTargetLinker provides a simple and extensible framework for biologists and bioinformaticians to integrate different regulatory interactions into their network analysis approaches. Visualization options enable biological interpretation of complex regulatory networks in a graphical way. Importantly the incorporation of our tool into the Cytoscape framework allows the application of CyTargetLinker in combination with a wide variety of other apps for state-of-the-art network analysis.

Dataset Information

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

Publications

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

Similar Datasets

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