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
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L1000 Viewer: A Search Engine and Web Interface for the LINCS Data Repository
TL;DR: The L1000 Viewer is developed, a search engine and graphical web interface for the LINCS L1000 data repository that serves as an interactive platform allowing the user to select different forms of perturbation profiles among the data files.
Journal ArticleDOI
Lymecycline reverses acquired EGFR-TKI resistance in non-small-cell lung cancer by targeting GRB2.
Yang Chen,Jie Wu,Hongfei Yan,Yang Cheng,Yizhe Wang,Yi Yang,Mingming Deng,Xiaofang Che,Kezuo Hou,Xiujuan Qu,Dan Zou,Yunpeng Liu,Ye Zhang,Xuejun Hu +13 more
TL;DR: There is strong support that Lymecycline when combined with EGFR targeting drugs, enhanced the efficacy of treatments for drug-resistant NSCLC and inhibited the resistance of the cell cycle to EGFR-TKI and induced apoptosis in NSCLCs.
Journal ArticleDOI
From Phenotypic Hit to Chemical Probe: Chemical Biology Approaches to Elucidate Small Molecule Action in Complex Biological Systems.
TL;DR: The need for chemical biologists to integrate and expand the existing tools to increase the probability of evolving screen hits to robust chemical probes is illustrated.
Journal ArticleDOI
The Cancer Dependency Map enables drug mechanism-of-action investigations.
Francisca Vazquez,Jesse S. Boehm +1 more
TL;DR: G Garnett and colleagues demonstrate proof‐of‐concept for a new way to attack this problem systematically for Oncology drugs, by identifying correlated CRISPR‐ and drug‐killing profiles in the Cancer Dependency Map dataset.
Journal ArticleDOI
Intraperitoneal Administration of Telmisartan Prevents Postsurgical Adhesion Band Formation.
Mohammad-Hassan Arjmand,Farnaz Zahedi-Avval,Farnaz Barneh,Seyed Hadi Mousavi,Fereshteh Asgharzadeh,Milad Hashemzehi,Atena Soleimani,Amir Avan,Maryam Fakhraie,Seyedeh Najibeh Nasiri,Saeedeh Mehraban,Gordon A. Ferns,Mikhail Ryzhikov,Mohieddin Jafari,Majid Khazaei,Seyed Mahdi Hassanian +15 more
TL;DR: These results support the potential application of telmisartan in preventing postsurgical adhesion band formation by inhibiting key pathologic responses of inflammation and fibrosis in postsurgery patients.
References
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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.
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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.
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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.
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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.
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