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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Journal ArticleDOI
Influence of batch effect correction methods on drug induced differential gene expression profiles
TL;DR: Batch effect correction methods strongly impact differential gene expression analysis when the sample size is large enough to contain sufficient information and thus the downstream drug repositioning and therefore recommend including two or three principal components as covariates in fitting models with limma when sample Size is sufficient.
Journal ArticleDOI
Functional Gene Module–Based Identification of Phillyrin as an Anticardiac Fibrosis Agent
TL;DR: The results showed that phillyrin was a novel antifibrotic agent in heart diseases, and this study aimed to construct a gene functional module to represent the core pathological process of CF and screen antifIBrotic agents capable of decreasing the expression of the genefunctional module.
Book ChapterDOI
An Application of Computational Drug Repurposing Based on Transcriptomic Signatures.
TL;DR: This chapter presents a step-by-step methodology of a transcriptomics-based computational drug repurposing pipeline providing a comprehensive guide to the whole procedure, from proper dataset selection to short list derivation of repurposed drugs which might act as inhibitors against the studied disease.
Journal ArticleDOI
Connecting omics signatures and revealing biological mechanisms with iLINCS
Marcin Pilarczyk,Mehdi Fazel-Najafabadi,Michal Kouril,Behrouz Shamsaei,Juozas Vasiliauskas,Wen Niu,Naim Al Mahi,Lixia Zhang,Nicholas A. Clark,Yan Ren,Shana White,Rashid Karim,Huan Xu,Jacek Biesiada,Mark F Bennett,Sarah E. Davidson,John F. Reichard,Kurt Roberts,Vasileios Stathias,Amar Koleti,Dusica Vidovic,Daniel J.B. Clarke,Stephan C. Schürer,Avi Ma'ayan,Jaroslaw Meller,Mario Medvedovic +25 more
TL;DR: i et al. as mentioned in this paper presented an integrative web-based platform for analysis of omics data and signatures of cellular perturbations, which facilitates mining and re-analysis of the large collection of omICS datasets, pre-computed signatures, and their connections.
Journal ArticleDOI
Systems Pharmacogenomic Landscape of Drug Similarities from LINCS data: Drug Association Networks
Aliyu Musa,Shailesh Tripathi,Matthias Dehmer,Olli Yli-Harja,Stuart A. Kauffman,Frank Emmert-Streib +5 more
TL;DR: This paper uses LINCS data to construct drug association networks (DANs) representing the relationships between drugs and identifies the modules of the DANs as therapeutic attractors of the ATC drug classes.
References
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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.
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