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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Integrative Metabolomic and Transcriptomic Analysis for the Study of Bladder Cancer
Alba Loras,Cristian Suárez-Cabrera,M. Carmen Martínez-Bisbal,Guillermo Quintás,Jesús M. Paramio,Ramón Martínez-Máñez,Salvador Gil,Salvador Gil,J.L. Ruiz-Cerdá,J.L. Ruiz-Cerdá +9 more
TL;DR: The urinary profiling study showed a relation with taurine and other amino acids perturbed pathways observed in BC tissue samples, and classified BC from non-tumor urine samples with good sensitivities and specificities, and could be used as a non-invasive tool for BC diagnosis and follow-up.
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Novel Long Noncoding RNA, Macrophage Inflammation-Suppressing Transcript (MIST), Regulates Macrophage Activation During Obesity
Kenneth Stapleton,Sadhan Das,Marpadga A. Reddy,Amy Leung,Vishnu Amaram,Linda Lanting,Zhuo Chen,Lingxiao Zhang,Rengasamy Palanivel,Jeffrey A. Deiuliis,Rama Natarajan +10 more
TL;DR: A top candidate long noncoding RNA, macrophage inflammation-suppressing transcript (Mist), was downregulated in both peritoneal macrophages and adipose tissue Macrophages from high-fat diet–fed mice and human orthologous MIST was also downregulated by proinflammatory stimuli.
Journal ArticleDOI
PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells.
Shuchi Agrawal Singh,Shuchi Agrawal Singh,Mads Lerdrup,Ana-Luisa R Gomes,Harmen J.G. van de Werken,Jens Vilstrup Johansen,Robin Andersson,Albin Sandelin,Kristian Helin,Kristian Helin,Klaus Hansen +10 more
TL;DR: A latent enhancer within the ZBTB16/PLZF locus itself that became active, gained PLZF, p300 and Mediator binding and looped to the promoter of the nicotinamide N-methyltransferase (NNMT) gene correlated with a decline in SAM levels, which is dependent on PLZf and is required for osteogenic differentiation.
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Genome-Wide Analysis Reveals Mucociliary Remodeling of the Nasal Airway Epithelium Induced by Urban PM2.5.
M.T. Montgomery,Satria Sajuthi,Seung-Hyun Cho,Jamie L. Everman,Cydney Rios,K.C. Goldfarbmuren,Nathan D. Jackson,B. Saef,Meghan Cromie,Celeste Eng,Vivian Medina,Jennifer R. Elhawary,Sam S. Oh,Jose R. Rodriguez-Santana,Eszter K. Vladar,Esteban G. Burchard,Max A. Seibold +16 more
TL;DR: It is found that PM2.5 organic extract, but not water-soluble, constituents elicited a potent, dose-dependent transcriptomic response from the mucociliary epithelium, and chronic OE stimulation induced mucus metaplasia-like remodeling characterized by increases in M UC5AC+ secretory cells and MUC5AC mucus secretions.
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PathwayConnector: finding complementary pathways to enhance functional analysis.
TL;DR: The proposed web-tool is a simple yet informative tool towards identifying connected groups of pathways that are significantly related to specific diseases.
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