A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.
Aravind Subramanian,Rajiv Narayan,Steven M. Corsello,Steven M. Corsello,David Peck,Ted Natoli,Xiaodong Lu,Joshua Gould,John F. Davis,Andrew A. Tubelli,Jacob K. Asiedu,David L. Lahr,Jodi E. Hirschman,Zihan Liu,Melanie Donahue,Bina Julian,Mariya Khan,David Wadden,Ian Smith,Daniel D. Lam,Arthur Liberzon,Courtney Toder,Mukta Bagul,Marek Orzechowski,Oana M. Enache,Federica Piccioni,Sarah A. Johnson,Nicholas J. Lyons,Alice H. Berger,Alice H. Berger,Alykhan F. Shamji,Angela N. Brooks,Angela N. Brooks,Anita Vrcic,Corey Flynn,Jacqueline Rosains,David Y. Takeda,David Y. Takeda,Roger Hu,Desiree Davison,Justin Lamb,Kristin Ardlie,Larson Hogstrom,Peyton Greenside,Nathanael S. Gray,Nathanael S. Gray,Paul A. Clemons,Serena J. Silver,Xiaoyun Wu,Wen-Ning Zhao,Wen-Ning Zhao,Willis Read-Button,Xiaohua Wu,Stephen J. Haggarty,Stephen J. Haggarty,Lucienne Ronco,Jesse S. Boehm,Stuart L. Schreiber,Stuart L. Schreiber,Stuart L. Schreiber,John G. Doench,Joshua A. Bittker,David E. Root,Bang Wong,Todd R. Golub +64 more
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TLDR
The expanded CMap is reported, made possible by a new, low-cost, high-throughput reduced representation expression profiling method that is shown to be highly reproducible, comparable to RNA sequencing, and suitable for computational inference of the expression levels of 81% of non-measured transcripts.About:
This article is published in Cell.The article was published on 2017-11-30 and is currently open access. It has received 1943 citations till now.read more
Citations
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Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations
Phuwanat Sakornsakolpat,Dmitry Prokopenko,Maxime Lamontagne,Nicola F. Reeve,Anna L. Guyatt,Victoria E. Jackson,Nick Shrine,Dandi Qiao,Traci M. Bartz,Deog Kyeom Kim,Mi Kyeong Lee,Jeanne C. Latourelle,Xingnan Li,Jarrett D. Morrow,Ma'en Obeidat,Annah B. Wyss,Per Bakke,R. Graham Barr,Terri H. Beaty,Steven A. Belinsky,Guy Brusselle,James D. Crapo,Kim de Jong,Dawn L. DeMeo,Tasha E. Fingerlin,Sina A. Gharib,Amund Gulsvik,Ian P. Hall,John E. Hokanson,Woo Jin Kim,David A. Lomas,Stephanie J. London,Deborah A. Meyers,George T. O'Connor,Rennard, Stephen, I,David A. Schwartz,Pawel Sliwinski,David Sparrow,David P. Strachan,Ruth Tal-Singer,Yohannes Tesfaigzi,Jørgen Vestbo,Judith M. Vonk,Jae-Joon Yim,Xiaobo Zhou,Yohan Bossé,Ani Manichaikul,Lies Lahousse,Edwin K. Silverman,H. Marike Boezen,Louise V. Wain,Martin D. Tobin,Brian D. Hobbs,Michael H. Cho,Chiara Batini,Jing Hua Zhao,Matthias Wielscher,Stefan Weiss,Katherine A. Kentistou,James P. Cook,Jennie Hui,Stefan Karrasch,Medea Imboden,Sarah E. Harris,Jonathan Marten,Stefan Enroth,Shona M. Kerr,Ida Surakka,Veronique Vitart,Terho Lehtimäki,Ralf Ewert,Christian Gieger,Georg Homuth,Peter K. Joshi,Claudia Langenberg,Lars Lind,Jian'an Luan,Anubha Mahajan,Alison D. Murray,David J. Porteous,Rajesh Rawal,Blair H. Smith,Paul R. H. J. Timmers,Olli T. Raitakari,Mika Kähönen,Ozren Polasek,Ulf Gyllensten,Igor Rudan,Ian J. Deary,Nicole Probst-Hensch,Holger Schulz,Alan James,James F. Wilson,Beate Stubbe,Eleftheria Zeggini,Marjo-Riitta Järvelin,Nicholas J. Wareham,Caroline Hayward,Andrew P. Morris,Alvar Agusti,Wayne Anderson,Nawar Diar Bakerly,Robert Bals,Kathleen C. Barnes,Eugene R. Bleecker,Russell P. Bowler,Christopher E. Brightling,Marleen de Bruijne,Peterj Castaldi,Bartolome R. Celli,Harvey O. Coxson,Ron Crystal,Pim de Jong,Asger Dirksen,Jennifer G. Dy,Marilyn G. Foreman,Judith Garcia-Aymerich,Pierre Gevenois,Soumitra Ghosh,Hester A. Gietema,Nadia N. Hansel,Craig P. Hersh,Eric A. Hoffman,Noor Kalsheker,Hans-Ulrich Kauczor,Tarja Laitinen,Diether Lambrechts,Augusto A. Litonjua,Daan W. Loth,Sharon M. Lutz,David A. Lynch,William MacNee,Merry-Lynn McDonald,John D. Newell,Børge G. Nordestgaard,Yeon-Mok Oh,Peter D. Paré,Massimo Pistolesi,Dirkje S. Postma,Milo A. Puhan,Elizabeth A. Regan,Stephen S. Rich,Joon Beom Seo,Andrea D. Short,Berend C. Stoel,Nicola Sverzellati,Gerben ter Riet,Edwin J R van Beek,Bram van Ginneken,Claus Vogelmeier,Adam Wanner,George R. Washko,Els Wauters,Emiel F.M. Wouters,Robert P. Young,Loems Zeigler-Heitbrock +155 more
TL;DR: Genome-wide analysis of chronic obstructive pulmonary disease identifies 82 loci, 35 of which are new, and integrates gene expression and genomic annotation data shows enrichment of signals in lung tissue, smooth muscle and several lung cell types.
Journal ArticleDOI
Cas9 activates the p53 pathway and selects for p53-inactivating mutations.
Oana M. Enache,Veronica Rendo,Mai Abdusamad,Daniel D. Lam,Desiree Davison,Sangita Pal,Naomi Currimjee,Julian M. Hess,Sasha Pantel,Anwesha Nag,Aaron R. Thorner,John G. Doench,Francisca Vazquez,Rameen Beroukhim,Rameen Beroukhim,Todd R. Golub,Uri Ben-David,Uri Ben-David +17 more
TL;DR: Genetic and transcriptional consequences of Cas9 expression induces DNA damage and activates the p53 pathway, and it can lead to the selection of cells with p53-inactivating mutations, and Cas9 is less active in wild-type TP53 cell lines than in TP53- mutant cell lines.
Journal ArticleDOI
Evaluation of RNAi and CRISPR technologies by large-scale gene expression profiling in the Connectivity Map.
Ian Smith,Peyton Greenside,Ted Natoli,David L. Lahr,David Wadden,Itay Tirosh,Rajiv Narayan,David E. Root,Todd R. Golub,Aravind Subramanian,John G. Doench +10 more
TL;DR: This work shows that mitigating off-target effects is feasible in these datasets via computational methodologies to produce a consensus gene signature (CGS) and compared RNAi technology to clustered regularly interspaced short palindromic repeat (CRISPR)-based knockout by analysis of 373 single guide RNAs (sgRNAs) to show that the on-target efficacies are comparable, but CRISPR technology is far less susceptible to systematic off- target effects.
Journal ArticleDOI
Integrated Proteogenomic Characterization across Major Histological Types of Pediatric Brain Cancer
Francesca Petralia,Nicole Tignor,Boris Reva,Mateusz Koptyra,Shrabanti Chowdhury,Dmitry Rykunov,Azra Krek,Weiping Ma,Yuankun Zhu,Jiayi Ji,Anna Calinawan,Jeffrey R. Whiteaker,Antonio Colaprico,Vasileios Stathias,Tatiana Omelchenko,Xiaoyu Song,Pichai Raman,Yiran Guo,Miguel A. Brown,Richard G. Ivey,John Szpyt,Sanjukta Guha Thakurta,Marina A. Gritsenko,Karl K. Weitz,Gonzalo Lopez,Selim Kalayci,Zeynep H. Gümüş,Seungyeul Yoo,Felipe da Veiga Leprevost,Hui Yin Chang,Karsten Krug,Lizabeth Katsnelson,Ying Wang,Jacob J. Kennedy,Uliana J. Voytovich,Lei Zhao,Krutika S. Gaonkar,Brian Ennis,Bo Zhang,Valerie Baubet,Lamiya Tauhid,Jena Lilly,Jennifer Mason,Bailey Farrow,Nathan Young,Sarah Leary,Sarah Leary,Sarah Leary,Jamie Moon,Vladislav A. Petyuk,Javad Nazarian,Javad Nazarian,Nithin D. Adappa,James N. Palmer,Robert Lober,Samuel Rivero-Hinojosa,Liang-Bo Wang,Joshua M. Wang,Matilda Broberg,Rosalie K. Chu,Ronald J. Moore,Matthew E. Monroe,Rui Zhao,Richard D. Smith,Jun Zhu,Ana I. Robles,Mehdi Mesri,Emily S. Boja,Tara Hiltke,Henry Rodriguez,Bing Zhang,Eric E. Schadt,D. R. Mani,Li Ding,Antonio Iavarone,Maciej Wiznerowicz,Maciej Wiznerowicz,Stephan C. Schürer,Xi Chen,Allison Heath,Jo Lynne Rokita,Alexey I. Nesvizhskii,David Fenyö,Karin D. Rodland,Karin D. Rodland,Tao Liu,Steven P. Gygi,Amanda G. Paulovich,Adam C. Resnick,Phillip B. Storm,Brian R. Rood,Pei Wang,Alicia Francis,Allison M. Morgan,Angela Waanders,Angela N. Viaene,Anna Maria Buccoliero,Arul M. Chinnaiyan,Carina A. Leonard,Cassie Kline,Chiara Caporalini,Christopher R. Kinsinger,Chunde Li,David E. Kram,Derek Hanson,Elizabeth Appert,Emily Kawaler,Eric H. Raabe,Eric M. Jackson,Jeffrey P. Greenfield,Gabrielle S. Stone,Gad Getz,Gerald A. Grant,Guo Ci Teo,Ian F. Pollack,Jason E. Cain,Jessica B. Foster,Joanna J. Phillips,July E. Palma,Karen A. Ketchum,Kelly V. Ruggles,Lili Blumenberg,MacIntosh Cornwell,Mahdi Sarmady,Marcin J. Domagalski,Marcin Cieślik,Mariarita Santi,Marilyn M. Li,Matthew J. Ellis,Matthew A. Wyczalkowski,Meghan Connors,Mirko Scagnet,Nalin Gupta,Nathan Edwards,Nicholas A Vitanza,Olena Morozova Vaske,Oren J. Becher,Peter B. McGarvey,Ron Firestein,Sabine Mueller,Samuel G. Winebrake,Saravana M. Dhanasekaran,Shuang Cai,Sonia Partap,Tatiana Patton,Toan Le,Travis D. Lorentzen,Wenke Liu,William Bocik +148 more
TL;DR: This is the first large-scale proteogenomics analysis across traditional histological boundaries to uncover foundational pediatric brain tumor biology and inform rational treatment selection.
Posted ContentDOI
Trans effects on gene expression can drive omnigenic inheritance
TL;DR: This work provides a formal model in which genetic contributions to complex traits can be partitioned into direct effects from core genes, and indirect effects from peripheral genes acting as trans-regulators, and proposes a framework for understanding key features of the architecture of complex traits.
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