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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Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome
Bernardo P. de Almeida,André Filipe Vieira,Joana Paredes,Mónica Bettencourt-Dias,Nuno L. Barbosa-Morais +4 more
TL;DR: It is shown that high CA20 is associated with poor prognosis and candidate compounds for selectively targeting cancer cells exhibiting transcriptomic evidence for CA are identified by integrating drug sensitivity with drug perturbation profiles in cell lines.
Journal ArticleDOI
Protein interaction and functional data indicate MTHFD2 involvement in RNA processing and translation
TL;DR: Findings suggest a novel function of MTHFD2 in RNA metabolism and translation, including components of the small ribosomal subunit and multiple members of the RNA-processing hnRNP family.
Journal ArticleDOI
A Proteomic Variant Approach (ProVarA) for Personalized Medicine of Inherited and Somatic Disease.
TL;DR: ProVarA represents the first comparative proteomic analysis among multiple disease-causing mutations, thereby providing a methodological approach that provides a significant advancement to existing proteomic efforts in understanding the impact of variation in CF disease.
Journal ArticleDOI
Transcriptomics in Toxicogenomics, Part III: Data Modelling for Risk Assessment
Angela Serra,Michele Fratello,Luca Cattelani,Irene Liampa,Georgia Melagraki,Pekka Kohonen,Penny Nymark,Antonio Federico,Pia Anneli Sofia Kinaret,Pia Anneli Sofia Kinaret,Karolina Jagiello,My Kieu Ha,My Kieu Ha,Jang-Sik Choi,Jang-Sik Choi,Natasha Sanabria,Mary Gulumian,Tomasz Puzyn,Tae Hyun Yoon,Tae Hyun Yoon,Haralambos Sarimveis,Roland C. Grafström,Antreas Afantitis,Dario Greco,Dario Greco +24 more
TL;DR: This review presents the state-of-the-art of data modelling applied to transcriptomics data in TGx, and shows how the benchmark dose (BMD) analysis can be applied to TGx data.
Journal ArticleDOI
Signature-based approaches for informed drug repurposing: targeting CNS disorders.
Rammohan Shukla,Nicholas D. Henkel,Khaled Alganem,Abdul-Rizaq Hamoud,James Reigle,Rawan Alnafisah,Hunter M. Eby,Ali S Imami,Justin F. Creeden,Scott A. Miruzzi,Jaroslaw Meller,Robert E. McCullumsmith +11 more
TL;DR: Various signature-based in silico approaches to drug repurposing, its integration with multiple omics platforms, and how this data can be used for clinically relevant, evidence-based drugRepurposing are discussed.
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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