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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YAP-independent mechanotransduction drives breast cancer progression.
Joanna Y. Lee,Jessica Chang,Antonia A. Dominguez,Hong-pyo Lee,Sungmin Nam,Julie Chang,Sushama Varma,Lei S. Qi,Robert B. West,Ovijit Chaudhuri +9 more
TL;DR: It is established that YAP does not mediate mechanotransduction in breast cancer, and mechanical signals are transduced independently of YAP, questioning YAP as a therapeutic target.
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Precursors for Nonlymphoid-Tissue Treg Cells Reside in Secondary Lymphoid Organs and Are Programmed by the Transcription Factor BATF
Michael Delacher,Michael Delacher,Charles D. Imbusch,Charles D. Imbusch,Agnes Hotz-Wagenblatt,Jan-Philipp Mallm,Katharina Bauer,Malte Simon,Malte Simon,Dania Riegel,André F. Rendeiro,Sebastian Bittner,Lieke Sanderink,Asmita Pant,Lisa Schmidleithner,Kathrin L. Braband,Bernd Echtenachter,Alexander Fischer,Valentina Giunchiglia,Valentina Giunchiglia,Petra Hoffmann,Matthias Edinger,Christoph Bock,Michael Rehli,Benedikt Brors,Christian Schmidl,Markus Feuerer,Markus Feuerer +27 more
TL;DR: This work identified two precursor stages of interleukin 33 (IL-33) receptor ST2-expressing nonlymphoid tissue Treg cells, which resided in the spleen and lymph nodes and validated the transcription factor Batf as the driver of the molecular tissue program in the precursors.
Journal ArticleDOI
Dopaminylation of histone H3 in ventral tegmental area regulates cocaine seeking
Ashley E. Lepack,Craig T. Werner,Andrew F. Stewart,Sasha L. Fulton,Ping Zhong,Lorna A. Farrelly,Alexander C.W. Smith,Aarthi Ramakrishnan,Yang Lyu,Ryan M. Bastle,Jennifer A. Martin,Swarup Mitra,Richard M. O'Connor,Zi-Jun Wang,Henrik Molina,Gustavo Turecki,Li Shen,Zhen Yan,Erin S. Calipari,David M. Dietz,Paul J. Kenny,Ian Maze +21 more
TL;DR: By reducing H3Q5dop in the VTA during withdrawal, this work reversed cocaine-mediated gene expression changes, attenuated dopamine release in the nucleus accumbens, and reduced cocaine-seeking behavior, establishing a neurotransmission-independent role for nuclear dopamine in relapse-related transcriptional plasticity in the rat ventral tegmental area.
Journal ArticleDOI
Dissecting heterogeneity in malignant pleural mesothelioma through histo-molecular gradients for clinical applications.
Yuna Blum,Clément Meiller,Clément Meiller,Lisa Quetel,Lisa Quetel,Nabila Elarouci,Mira Ayadi,Danisa Tashtanbaeva,Danisa Tashtanbaeva,Lucile Armenoult,François Montagne,Robin Tranchant,Robin Tranchant,Robin Tranchant,Annie Renier,Annie Renier,Leanne de Koning,Marie-Christine Copin,Paul Hofman,Véronique Hofman,Henri Porte,Françoise Le Pimpec-Barthes,Jessica Zucman-Rossi,Jessica Zucman-Rossi,Marie-Claude Jaurand,Marie-Claude Jaurand,Aurélien de Reyniès,Didier Jean,Didier Jean +28 more
TL;DR: It is shown that each tumor can be decomposed as a combination of epithelioid-like and sarcomatoid-like components whose proportions are highly associated with the prognosis and could inform therapeutic strategies.
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The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins.
Kushal Suryamohan,Sajesh Puthenpurackal Krishnankutty,Joseph Guillory,Matthew Jevit,Markus S. Schröder,Meng Wu,Boney Kuriakose,Oommen K. Mathew,Rajadurai Chinnasamy Perumal,Ivan Koludarov,Leonard D. Goldstein,Kate Senger,Mandumpala Davis Dixon,Dinesh Velayutham,Derek Vargas,Subhra Chaudhuri,Megha Muraleedharan,Ridhi Goel,Ying Jiun J. Chen,Aakrosh Ratan,Peter Liu,Brendan Faherty,Guillermo de la Rosa,Hiroki Shibata,Miriam Baca,Meredith Sagolla,James Ziai,Gus A. Wright,Domagoj Vucic,Sangeetha Mohan,Aju Antony,Jeremy Stinson,Donald S. Kirkpatrick,Rami N. Hannoush,Steffen Durinck,Zora Modrusan,Eric Stawiski,Kristen Wiley,Terje Raudsepp,R. Manjunatha Kini,Arun Zachariah,Somasekar Seshagiri +41 more
TL;DR: The genome of Naja naja, the Indian cobra, a highly venomous, medically important snake, is reported, which could serve as a reference for snake genomes, support evolutionary studies and enable venom-driven drug discovery.
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