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dc.contributor.authorHu, Yanhuien_US
dc.contributor.authorComjean, Aramen_US
dc.contributor.authorPerrimon, Norberten_US
dc.contributor.authorMohr, Stephanie E.en_US
dc.date.accessioned2017-03-28T23:50:45Z
dc.date.issued2017en_US
dc.identifier.citationHu, Yanhui, Aram Comjean, Norbert Perrimon, and Stephanie E. Mohr. 2017. “The Drosophila Gene Expression Tool (DGET) for expression analyses.” BMC Bioinformatics 18 (1): 98. doi:10.1186/s12859-017-1509-z. http://dx.doi.org/10.1186/s12859-017-1509-z.en
dc.identifier.issnen
dc.identifier.urihttp://nrs.harvard.edu/urn-3:HUL.InstRepos:31731813
dc.description.abstractBackground: Next-generation sequencing technologies have greatly increased our ability to identify gene expression levels, including at specific developmental stages and in specific tissues. Gene expression data can help researchers understand the diverse functions of genes and gene networks, as well as help in the design of specific and efficient functional studies, such as by helping researchers choose the most appropriate tissue for a study of a group of genes, or conversely, by limiting a long list of gene candidates to the subset that are normally expressed at a given stage or in a given tissue. Results: We report DGET, a Drosophila Gene Expression Tool (www.flyrnai.org/tools/dget/web/), which stores and facilitates search of RNA-Seq based expression profiles available from the modENCODE consortium and other public data sets. Using DGET, researchers are able to look up gene expression profiles, filter results based on threshold expression values, and compare expression data across different developmental stages, tissues and treatments. In addition, at DGET a researcher can analyze tissue or stage-specific enrichment for an inputted list of genes (e.g., ‘hits’ from a screen) and search for additional genes with similar expression patterns. We performed a number of analyses to demonstrate the quality and robustness of the resource. In particular, we show that evolutionary conserved genes expressed at high or moderate levels in both fly and human tend to be expressed in similar tissues. Using DGET, we compared whole tissue profile and sub-region/cell-type specific datasets and estimated a potential source of false positives in one dataset. We also demonstrated the usefulness of DGET for synexpression studies by querying genes with expression profile similar to the mesodermal master regulator Twist. Conclusion: Altogether, DGET provides a flexible tool for expression data retrieval and analysis with short or long lists of Drosophila genes, which can help scientists to design stage- or tissue-specific in vivo studies and do other subsequent analyses.en
dc.language.isoen_USen
dc.publisherBioMed Centralen
dc.relation.isversionofdoi:10.1186/s12859-017-1509-zen
dc.relation.hasversionhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC5303223/pdf/en
dash.licenseLAAen_US
dc.subjectDrosophilaen
dc.subjectRNA-Seqen
dc.subjectExpression profileen
dc.subjectSynexpressionen
dc.titleThe Drosophila Gene Expression Tool (DGET) for expression analysesen
dc.typeJournal Articleen_US
dc.description.versionVersion of Recorden
dc.relation.journalBMC Bioinformaticsen
dash.depositing.authorHu, Yanhuien_US
dc.date.available2017-03-28T23:50:45Z
dc.identifier.doi10.1186/s12859-017-1509-z*
dash.contributor.affiliatedComjean, Aram
dash.contributor.affiliatedMohr, Stephanie
dash.contributor.affiliatedHu, Yanhui
dash.contributor.affiliatedPerrimon, Norbert


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