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      FlyRNAi.org—the database of the Drosophila RNAi screening center and transgenic RNAi project: 2017 update

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          Abstract

          The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and Transgenic RNAi Project (TRiP) at Harvard Medical School and associated DRSC/TRiP Functional Genomics Resources website ( http://fgr.hms.harvard.edu) serve as a reagent production tracking system, screen data repository, and portal to the community. Through this portal, we make available protocols, online tools, and other resources useful to researchers at all stages of high-throughput functional genomics screening, from assay design and reagent identification to data analysis and interpretation. In this update, we describe recent changes and additions to our website, database and suite of online tools. Recent changes reflect a shift in our focus from a single technology (RNAi) and model species ( Drosophila) to the application of additional technologies (e.g. CRISPR) and support of integrated, cross-species approaches to uncovering gene function using functional genomics and other approaches.

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          Identification of functional elements and regulatory circuits by Drosophila modENCODE.

          Sushmita Roy, Jason Ernst, Peter V. Kharchenko … (2011)
          To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and tissue-specific regulators, and enables gene-expression prediction. Our results provide a foundation for directed experimental and computational studies in Drosophila and related species and also a model for systematic data integration toward comprehensive genomic and functional annotation.
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            JBrowse: a dynamic web platform for genome visualization and analysis

            Robert Buels, Eric Yao, Colin Diesh … (2016)
            Background JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. Results Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. Conclusions JBrowse is a mature web application suitable for genome visualization and analysis.
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              PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

              Huaiyu Mi, Jun-Qing Dong, Anushya Muruganujan … (2010)
              Protein Analysis THrough Evolutionary Relationships (PANTHER) is a comprehensive software system for inferring the functions of genes based on their evolutionary relationships. Phylogenetic trees of gene families form the basis for PANTHER and these trees are annotated with ontology terms describing the evolution of gene function from ancestral to modern day genes. One of the main applications of PANTHER is in accurate prediction of the functions of uncharacterized genes, based on their evolutionary relationships to genes with functions known from experiment. The PANTHER website, freely available at http://www.pantherdb.org, also includes software tools for analyzing genomic data relative to known and inferred gene functions. Since 2007, there have been several new developments to PANTHER: (i) improved phylogenetic trees, explicitly representing speciation and gene duplication events, (ii) identification of gene orthologs, including least diverged orthologs (best one-to-one pairs), (iii) coverage of more genomes (48 genomes, up to 87% of genes in each genome; see http://www.pantherdb.org/panther/summaryStats.jsp), (iv) improved support for alternative database identifiers for genes, proteins and microarray probes and (v) adoption of the SBGN standard for display of biological pathways. In addition, PANTHER trees are being annotated with gene function as part of the Gene Ontology Reference Genome project, resulting in an increasing number of curated functional annotations.
              Article 0 comments Cited 269 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (hwp): nar
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 04 January 2017
                Publication date (Electronic): 23 October 2016
                Publication date PMC-release: 23 October 2016
                Volume: 45
                Issue: Database issue , Database issue
                Pages: D672-D678
                Affiliations
                [1 ]Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
                [2 ] Drosophila RNAi Screening Center and Transgenic RNAi Project, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
                [3 ]Marine Science Center, Northeastern University, 430 Nahant Rd., Nahant, MA 01908, USA
                [4 ]Howard Hughes Medical Institute, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
                Author notes
                [* ]To whom correspondence should be addressed. Tel: +1 617 432 5626; Fax: +1 617 432 7688; Email: stephanie_mohr@ 123456hms.harvard.edu
                Article
                DOI: 10.1093/nar/gkw977
                PMC ID: 5210654
                PubMed ID: 27924039
                SO-VID: 2767fc9a-fdfa-43b9-8a8c-a7e908aa6980
                Copyright © © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                Date accepted : 11 October 2016
                Date revision received : 05 October 2016
                Date received : 15 August 2016
                Page count
                Pages: 7
                Categories
                Subject: Database Issue
                Custom metadata
                cover-date 04 January 2017

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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