Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
Maxim V. Kuleshov,Matthew R. Jones,Andrew D. Rouillard,Nicolas F. Fernandez,Qiaonan Duan,Zichen Wang,Simon Koplev,Sherry L. Jenkins,Kathleen M. Jagodnik,Alexander Lachmann,Michael G. McDermott,Caroline D. Monteiro,Gregory W. Gundersen,Avi Ma'ayan +13 more
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TLDR
A significant update to one of the tools in this domain called Enrichr, a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries is presented.Abstract:
Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.read more
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Single-platform 'multi-omic' profiling: unified mass spectrometry and computational workflows for integrative proteomics-metabolomics analysis.
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Ye Liu,Jen-Chien Chang,Chung-Chau Hon,Naoshi Fukui,Nobuho Tanaka,Zhenya Zhang,Ming Ta Michael Lee,Aki Minoda +7 more
TL;DR: It is demonstrated how direct chromatin profiling of clinical tissues can provide comprehensive epigenetic information for a disease and suggest candidate genes and enhancers of translational potential for OA.
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Transcriptional and physiological adaptations in nucleus accumbens somatostatin interneurons that regulate behavioral responses to cocaine.
Efrain Ribeiro,Marine Salery,Joseph R. Scarpa,Erin S. Calipari,Peter J. Hamilton,Stacy M. Ku,Stacy M. Ku,Hope Kronman,Immanuel Purushothaman,Barbara Juarez,Mitra Heshmati,Marie A Doyle,Casey Lardner,Dominicka Burek,Ana N. Strat,Stephen T. Pirpinias,Ezekiell Mouzon,Ming-Hu Han,Ming-Hu Han,Rachael L. Neve,Rosemary C. Bagot,Rosemary C. Bagot,Andrew Kasarskis,Ja Wook Koo,Eric J. Nestler +24 more
TL;DR: It is found that the activity of somatostatin interneurons regulates behavioral responses to cocaine, with repeated cocaine reducing the excitability of these neurons.
Journal ArticleDOI
Loss of UGP2 in brain leads to a severe epileptic encephalopathy, emphasizing that bi-allelic isoform-specific start-loss mutations of essential genes can cause genetic diseases
Elena Perenthaler,Anita Nikoncuk,Soheil Yousefi,Woutje M. Berdowski,Maysoon Alsagob,Ivan Čapo,Herma C. van der Linde,Paul van den Berg,Edwin H. Jacobs,Darija Putar,Mehrnaz Ghazvini,Eleonora Aronica,Wilfred F. J. van IJcken,Walter G. de Valk,Evita Medici-van den Herik,Marjon van Slegtenhorst,Lauren Brick,Mariya Kozenko,Jennefer N. Kohler,Jonathan A. Bernstein,Kristin G. Monaghan,Amber Begtrup,Rebecca I. Torene,Amna Al Futaisi,Fathiya Al Murshedi,Renjith Mani,Faisal Al Azri,Erik-Jan Kamsteeg,Majid Mojarrad,Atieh Eslahi,Zaynab Khazaei,Fateme Massinaei Darmiyan,Mohammad Doosti,Ehsan Ghayoor Karimiani,Ehsan Ghayoor Karimiani,Jana Vandrovcova,Faisal Zafar,Nuzhat Rana,Krishna Kumar Kandaswamy,Jozef Hertecant,Peter Bauer,Mohammed A. AlMuhaizea,Mustafa A. Salih,Mazhor Al-Dosary,Rawan Almass,Laila AlQuait,Wafa Qubbaj,Serdar Coskun,Khaled O. Alahmadi,Muddathir H. Hamad,Salem Alwadaee,Khalid Awartani,Anas M. Dababo,Futwan Al-Mohanna,Dilek Colak,Mohammadreza Dehghani,Mohammad Yahya Vahidi Mehrjardi,Murat Gunel,A. Gulhan Ercan-Sencicek,Gouri Rao Passi,Huma Arshad Cheema,Stephanie Efthymiou,Henry Houlden,Aida M. Bertoli-Avella,Alice S. Brooks,Kyle Retterer,Reza Maroofian,Namik Kaya,Tjakko J. van Ham,Tahsin Stefan Barakat +69 more
TL;DR: This study identifies a recurrent start codon mutation in UGP2 as a cause of a novel autosomal recessive DEE syndrome and shows that isoform-specific start-loss mutations causing expression loss of a tissue-relevant isoform of an essential protein can cause a genetic disease, even when an organism-wide protein absence is incompatible with life.
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