ALBERT

Description: Autoantibodies target the RNA binding protein Ro60 in systemic lupus erythematosus (SLE) and Sjogren's syndrome. However, it is unclear whether Ro60 and its associated RNAs contribute to disease pathogenesis. We catalogued the Ro60-associated RNAs in human cell lines and found that among other RNAs, Ro60 bound an RNA motif derived from endogenous Alu retroelements. Alu transcripts were induced by type I interferon and stimulated proinflammatory cytokine secretion by human peripheral blood cells. Ro60 deletion resulted in enhanced expression of Alu RNAs and interferon-regulated genes. Anti-Ro60-positive SLE immune complexes contained Alu RNAs, and Alu transcripts were up-regulated in SLE whole blood samples relative to controls. These findings establish a link among the lupus autoantigen Ro60, Alu retroelements, and type I interferon.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691329/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691329/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hung, T -- Pratt, G A -- Sundararaman, B -- Townsend, M J -- Chaivorapol, C -- Bhangale, T -- Graham, R R -- Ortmann, W -- Criswell, L A -- Yeo, G W -- Behrens, T W -- HG004659/HG/NHGRI NIH HHS/ -- HG007005/HG/NHGRI NIH HHS/ -- NS075449/NS/NINDS NIH HHS/ -- R01 GM084317/GM/NIGMS NIH HHS/ -- R01 HG004659/HG/NHGRI NIH HHS/ -- R01 NS075449/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2015 Oct 23;350(6259):455-9. doi: 10.1126/science.aac7442. Epub 2015 Sep 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genentech, South San Francisco, CA 94080, USA. behrens.tim@gene.com hungt2@gene.com geneyeo@ucsd.edu. ; Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, University of California at San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA. ; Genentech, South San Francisco, CA 94080, USA. ; Rosalind Russell/Ephraim P. Engleman Rheumatology Research Center, University of California, San Francisco, CA 94143, USA. ; Department of Cellular and Molecular Medicine, Institute for Genomic Medicine, Stem Cell Program, University of California at San Diego, Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA 92037, USA. Department of Physiology, National University of Singapore, Singapore. Genome Institute of Singapore and Molecular Engineering Laboratory, Agency for Science, Technology and Research, Singapore. behrens.tim@gene.com hungt2@gene.com geneyeo@ucsd.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26382853" target="_blank"〉PubMed〈/a〉

Description: : It is common for computational analyses to generate large amounts of complex data that are difficult to process and share with collaborators. Standard methods are needed to transform such data into a more useful and intuitive format. We present ReportingTools, a Bioconductor package, that automatically recognizes and transforms the output of many common Bioconductor packages into rich, interactive, HTML-based reports. Reports are not generic, but have been individually designed to reflect content specific to the result type detected. Tabular output included in reports is sortable, filterable and searchable and contains context-relevant hyperlinks to external databases. Additionally, in-line graphics have been developed for specific analysis types and are embedded by default within table rows, providing a useful visual summary of underlying raw data. ReportingTools is highly flexible and reports can be easily customized for specific applications using the well-defined API. Availability : The ReportingTools package is implemented in R and available from Bioconductor (version ≥ 2.11) at the URL: http://bioconductor.org/packages/release/bioc/html/ReportingTools.html . Installation instructions and usage documentation can also be found at the above URL. Contact : hackney.jason@gene.com or kaminker.josh@gene.com