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
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Harnessing the biological complexity of Big Data from LINCS gene expression signatures
Aliyu Musa,Shailesh Tripathi,Shailesh Tripathi,Meenakshisundaram Kandhavelu,Matthias Dehmer,Frank Emmert-Streib +5 more
TL;DR: The gene expression signature profiles from all cell lines and their perturbagents are studied in order to obtain insights in the distributional characteristics of available conditions and help the experimental design of follow-up studies, e.g., by selecting appropriate cell lines.
Journal ArticleDOI
Reconciling multiple connectivity scores for drug repurposing.
TL;DR: In this paper, the authors present a systematic reconciliation of multiple disease-drug similarity metrics (ES, $css, $Sum, $Cosine, $XSum, XCor, XSpe, XCos, $EWCos$) and connectivity scores (CS, $RGES, $NCS, $Tau, $CSS, $EMUDRA), by defining them using consistent notation and terminology.
Journal ArticleDOI
Transcriptomic RNAseq drug screen in cerebrocortical cultures: toward novel neurogenetic disease therapies.
Jeremiah Hadwen,Jeremiah Hadwen,Sarah C. Schock,Sarah C. Schock,Alan J. Mears,Alan J. Mears,Robert Yang,Philippe Charron,Philippe Charron,Liying Zhang,Hualin S. Xi,Alex MacKenzie,Alex MacKenzie +12 more
TL;DR: A transcriptome-wide searchable database is created for easy access to the gene expression data resulting from the cerebrocortical drug screen and a novel link between thyroid hormone and expression of the peripheral neuropathy associated gene Pmp22 is identified.
Journal ArticleDOI
Identification of proteasome inhibitors using analysis of gene expression profiles.
TL;DR: The combination of bioinformatic analyses and cellular assays resulted in the identification of compounds with potential to inhibit the ubiquitin-proteasome system (UPS), suggesting other effects on the UPS.
Journal ArticleDOI
Downregulated CLIP3 induces radioresistance by enhancing stemness and glycolytic flux in glioblastoma
Hyunkoo Kang,Sungmin Lee,Kyeongmin Kim,Jaewan Jeon,Seok Gu Kang,HyeSook Youn,Hae Yu Kim,BuHyun Youn +7 more
TL;DR: In this paper, the effects of glimepiride combined with radiotherapy on GBM stem-like cells (GSCs) were investigated in a GBM orthotopic xenograft mouse model.
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.
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.
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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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