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
Reads0
Chats0
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
Mitigating temozolomide resistance in glioblastoma via DNA damage-repair inhibition.
TL;DR: A mechanistic mathematical model is developed that explicitly incorporates the effects of chemotherapy on tumour cells, including the processes of DNA damage induction, cell arrest and DNA repair, which has the potential to offset chemotherapy resistance in patients with glioblastoma and improve overall survival.
Journal ArticleDOI
Morphology and gene expression profiling provide complementary information for mapping cell state
TL;DR: In this article , the authors used both the L1000 and Cell Painting assays to profile gene expression and cell morphology, respectively, and applied unsupervised and supervised methods to predict compound mechanisms of action (MOAs) and gene targets, finding that the two assays not only provided a partially shared but also a complementary view of drug mechanisms.
Journal ArticleDOI
Characterization of cancer omics and drug perturbations in panels of lung cancer cells.
Ayako Suzuki,Keiichi Onodera,Keiichi Onodera,Ken Matsui,Ken Matsui,Masahide Seki,Hiroyasu Esumi,Tomoyoshi Soga,Sumio Sugano,Takashi Kohno,Yutaka Suzuki,Katsuya Tsuchihara +11 more
TL;DR: A stress response module that may be a promising drug intervention target is identified, as new combinations of compounds that could be used to regulate this module and the consequent phenotypic appearance of cancer cells have been identified.
Journal ArticleDOI
Development of Orthogonal Linear Separation Analysis (OLSA) to Decompose Drug Effects into Basic Components.
TL;DR: The potential of OLSA to decompose the effects of a drug and identify its basic components is indicated, including PI3K/AKT/mTORC1 inhibition activity, and other analyses including western blotting revealed that 4 of the 5 actually induced autophagy.
Journal ArticleDOI
Connectivity mapping of glomerular proteins identifies dimethylaminoparthenolide as a new inhibitor of diabetic kidney disease.
Julie Klein,Julie Klein,Cécile Caubet,Cécile Caubet,Mylène Camus,Manousos Makridakis,Colette Denis,Colette Denis,Marion Gilet,Marion Gilet,Guylène Feuillet,Guylène Feuillet,Simon Rascalou,Simon Rascalou,Eric Neau,Eric Neau,Luc Garrigues,Olivier Thillaye du Boullay,Harald Mischak,Bernard Monsarrat,Odile Burlet-Schiltz,Antonia Vlahou,Jean Sébastien Saulnier-Blache,Jean Sébastien Saulnier-Blache,Jean-Loup Bascands,Joost P. Schanstra,Joost P. Schanstra +26 more
TL;DR: Using a system biology approach, DMAPT, a water-soluble analogue of parthenolide, was identified as a compound with a potential add-on value to standard-of-care ACEi-treatment in DKD, in contrast to ramipril.
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