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
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
More filters
Journal ArticleDOI
Genome-wide association analyses of post-traumatic stress disorder and its symptom subdomains in the Million Veteran Program.
Murray B. Stein,Murray B. Stein,Daniel F. Levey,Zhongshan Cheng,Frank R. Wendt,Kelly M. Harrington,Kelly M. Harrington,Gita A. Pathak,Kelly Cho,Kelly Cho,Rachel Quaden,Krishnan Radhakrishnan,Krishnan Radhakrishnan,Matthew J. Girgenti,Yuk-Lam Ho,Daniel C Posner,Mihaela Aslan,Ronald S. Duman,Hongyu Zhao,VA Million Veteran Program,VA Million Veteran Program,Renato Polimanti,John Concato,John Concato,Joel Gelernter +24 more
TL;DR: This paper conducted genome-wide association analyses of over 250,000 participants of European and African ancestry from the Million Veteran Program using electronic health record-validated post-traumatic stress disorder (PTSD) diagnosis and quantitative symptom phenotypes.
Journal ArticleDOI
L1000FWD: fireworks visualization of drug-induced transcriptomic signatures
TL;DR: L1000FWD serves as a platform for identifying functions for novel small molecules using unsupervised clustering, as well as for exploring drug MOA in a promising approach toward revealing the mechanisms‐of‐action (MOA) for marketed drugs and other less studied potential therapeutic compounds.
Posted ContentDOI
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients
Anna C. Aschenbrenner,Anna C. Aschenbrenner,Maria Mouktaroudi,Benjamin Krämer,Nikolaos Antonakos,Marie Oestreich,Konstantina Gkizeli,Melanie Nuesch-Germano,Maria Saridaki,Lorenzo Bonaguro,Nico Reusch,Kevin Baßler,Sarandia Doulou,Rainer Knoll,Tal Pecht,Theodore S. Kapellos,Nikoletta Rovina,Charlotte Kröger,Miriam Herbert,Lisa Holsten,Arik Horne,Ioanna D. Gemünd,Shobhit Agrawal,Kilian Dahm,Martina van Uelft,Anna Drews,Lena Lenkeit,Niklas Bruse,Jelle Gerretsen,Jannik Gierlich,Matthias Becker,Kristian Händler,Michael Kraut,Heidi Theis,Simachew Mengiste,Elena De Domenico,Jonas Schulte-Schrepping,Lea Seep,Jan Raabe,Christoph Hoffmeister,Michael ToVinh,Verena Keitel,Gereon Rieke,Valentina Talevi,N. Ahmad Aziz,N. Ahmad Aziz,Peter Pickkers,Frank L. van de Veerdonk,Mihai G. Netea,Mihai G. Netea,Joachim L. Schultze,Joachim L. Schultze,Matthijs Kox,Monique M.B. Breteler,Monique M.B. Breteler,Jacob Nattermann,Antonia Koutsoukou,Evangelos J. Giamarellos-Bourboulis,Thomas Ulas,Thomas Ulas,German Covid Omics Initiative +60 more
TL;DR: Comparison of COVID-19 blood transcriptomes with those of a collection of over 2,600 samples derived from 11 different viral infections, inflammatory diseases and independent control samples revealed highly specific transcriptome signatures for CO VID-19, which predicted patient subgroup-specific drug candidates targeting the dysregulated systemic immune response of the host.
Journal ArticleDOI
Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition
Yael Cohen-Sharir,James M. McFarland,Mai Abdusamad,Carolyn Marquis,Sara Vanessa Bernhard,Mariya Kazachkova,Helen Tang,Marica Rosaria Ippolito,Kathrin Laue,Johanna Zerbib,Heidi L.H. Malaby,Andrew Jones,Lisa-Marie Stautmeister,Irena Bockaj,René Wardenaar,Nicholas J. Lyons,Ankur K. Nagaraja,Ankur K. Nagaraja,Adam J. Bass,Adam J. Bass,Diana C.J. Spierings,Floris Foijer,Rameen Beroukhim,Rameen Beroukhim,Stefano Santaguida,Stefano Santaguida,Todd R. Golub,Todd R. Golub,Jason Stumpff,Zuzana Storchova,Uri Ben-David +30 more
TL;DR: In this paper, aneuploid cancer cells exhibited aberrant spindle geometry and dynamics, and kept dividing when the SAC was inhibited, resulting in the accumulation of mitotic defects, and in unstable and less-fit karyotypes.
Journal ArticleDOI
Identification and application of gene expression signatures associated with lifespan extension
Alexander Tyshkovskiy,Perinur Bozaykut,A. A. Borodinova,Maxim V. Gerashchenko,Gene P. Ables,Michael Garratt,Philipp Khaitovich,Clary B. Clish,Richard A. Miller,Vadim N. Gladyshev,Vadim N. Gladyshev +10 more
TL;DR: General and specific transcriptomic programs of lifespan extension in mice are described and tools to discover new interventions are provided, including an app that visualizes associations between gene expression changes and longevity.
References
More filters
Journal ArticleDOI
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
Aravind Subramanian,Pablo Tamayo,Vamsi K. Mootha,Sayan Mukherjee,Benjamin L. Ebert,Michael A. Gillette,Amanda G. Paulovich,Scott L. Pomeroy,Todd R. Golub,Eric S. Lander,Jill P. Mesirov +10 more
TL;DR: The Gene Set Enrichment Analysis (GSEA) method as discussed by the authors focuses on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation.
Journal Article
Visualizing Data using t-SNE
TL;DR: A new technique called t-SNE that visualizes high-dimensional data by giving each datapoint a location in a two or three-dimensional map, a variation of Stochastic Neighbor Embedding that is much easier to optimize, and produces significantly better visualizations by reducing the tendency to crowd points together in the center of the map.
Journal ArticleDOI
Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
TL;DR: The Gene Expression Omnibus (GEO) project was initiated in response to the growing demand for a public repository for high-throughput gene expression data and provides a flexible and open design that facilitates submission, storage and retrieval of heterogeneous data sets from high-power gene expression and genomic hybridization experiments.
Journal ArticleDOI
BLAT—The BLAST-Like Alignment Tool
TL;DR: How BLAT was optimized is described, which is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
Journal ArticleDOI
Adjusting batch effects in microarray expression data using empirical Bayes methods
TL;DR: This paper proposed parametric and non-parametric empirical Bayes frameworks for adjusting data for batch effects that is robust to outliers in small sample sizes and performs comparable to existing methods for large samples.
Related Papers (5)
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Jordi Barretina,Giordano Caponigro,Nicolas Stransky,Kavitha Venkatesan,Adam A. Margolin,Adam A. Margolin,Sungjoon Kim,Christine D. Wilson,Joseph Lehar,Gregory V. Kryukov,Dmitriy Sonkin,Anupama Reddy,Manway Liu,Lauren Murray,Michael F. Berger,Michael F. Berger,John Monahan,Paula Morais,Jodi Meltzer,Adam Korejwa,Judit Jané-Valbuena,Judit Jané-Valbuena,Felipa A. Mapa,Joseph Thibault,Eva Bric-Furlong,Pichai Raman,Aaron Shipway,Ingo H. Engels,Jill Cheng,Guoying K. Yu,Jianjun Yu,Peter Aspesi,Melanie de Silva,Kalpana Jagtap,Michael D. Jones,Li Wang,Charlie Hatton,Emanuele Palescandolo,Supriya Gupta,Scott Mahan,Carrie Sougnez,Robert C. Onofrio,Ted Liefeld,Laura E. MacConaill,Wendy Winckler,Michael R. Reich,Nanxin Li,Jill P. Mesirov,Stacey Gabriel,Gad Getz,Kristin G. Ardlie,Vivien W. Chan,Vic E. Myer,Barbara L. Weber,Jeffrey A. Porter,Markus Warmuth,Peter Finan,Jennifer L. Harris,Matthew Meyerson,Matthew Meyerson,Todd R. Golub,Michael Morrissey,William R. Sellers,Robert Schlegel,Levi A. Garraway,Levi A. Garraway +65 more