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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Whole blood transcriptomic profiling identifies molecular pathways related to cardiovascular mortality in heart failure
Mintu Nath,Simon P. R. Romaine,Andrea Koekemoer,Stephen E. Hamby,Tom R. Webb,Christopher P. Nelson,Marcos Castellanos-Uribe,M. Papakonstantinou,Stefan D. Anker,Chim C. Lang,Marco Metra,Faiez Zannad,Gerasimos Filippatos,Dirk J. van Veldhuisen,John G.F. Cleland,Leong L. Ng,Sean T. May,Federica M. Marelli-Berg,Adriaan A. Voors,James A. Timmons,Nilesh J. Samani +20 more
TL;DR: This work investigated whether whole blood transcriptomic profiling can provide new mechanistic insights into cardiovascular (CV) mortality in CHF.
Journal ArticleDOI
ChemPert: mapping between chemical perturbation and transcriptional response for non-cancer cells
TL;DR: ChemPert is presented, a database consisting of 82270 transcriptional signatures across 167 non- cancer cell types, enabling more accurate predictions of perturbation responses and drugs compared to cancer databases in non-cancer cells, and provides a valuable resource for drug discovery innon-cancer diseases.
Journal ArticleDOI
Comprehensive analysis of key biomarkers, immune infiltration and potential therapeutic agents for ulcerative colitis.
TL;DR: Novel biomarkers and potential therapeutic agents for ulcerative colitis incidence worldwide are explored and meclofenamic acid is selected for its therapeutic effect on UC treatment by animal experiments.
Journal ArticleDOI
Novel Insights into Redox-Based Mechanisms for Auranofin-Induced Rapid Cancer Cell Death
Elie Hatem,Nadine El Banna,Amélie Heneman-Masurel,Dorothée Baïlle,Laurence Vernis,Sylvie Riquier,Marie-Pierre Golinelli-Cohen,Olivier Guittet,Cindy Vallières,Jean-Michel Camadro,Xue Qiu,Niko Hildebrandt,Michel Lepoivre,Meng-Er Huang +13 more
TL;DR: A new spectrum of AUF-induced early effects is shown and should provide novel insights into the complex redox-based mechanisms of this promising anticancer molecule.
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Transcriptome analysis and connectivity mapping of Cissampelos pareira L. provides molecular links of ESR1 modulation to viral inhibition.
Madiha Haider,Madiha Haider,Dhwani Dholakia,Dhwani Dholakia,Aleksha Panwar,Parth Garg,Atish Gheware,Atish Gheware,Dayanidhi Singh,Dayanidhi Singh,Khushboo Singhal,Khushboo Singhal,Shaunak A Burse,Shaunak A Burse,Surekha Kumari,Surekha Kumari,Anmol Sharma,Anmol Sharma,Arjun Ray,Guruprasad R. Medigeshi,Upendra Sharma,Upendra Sharma,Bhavana Prasher,Bhavana Prasher,Mitali Mukerji +24 more
TL;DR: In this article, the molecular basis of action of one such herbal formulation Cissampelos pareira L. (Cipa), used for the treatment of female hormone disorders and fever, was explored.
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.
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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
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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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