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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Book ChapterDOI
Guidelines for Setting Up a mRNA Sequencing Experiment and Best Practices for Bioinformatic Data Analysis.
TL;DR: The chapter proposes guidelines for completing a mRNA-seq study properly and makes available recommendations for best practices based on recent literature and on the latest developments in technology and algorithms.
Posted ContentDOI
The efficacy of chemotherapy is limited by intratumoural senescent cells that persist through the upregulation of PD-L2
Selim Chaib,Jose Alberto Lopez-Dominguez,Marta Lalinde,Neus Prats,Ines Cambra Marin,Kathleen Meyer,M I Munoz,Mònica Aguilera,Lidia Mateo,Camille Stephan-Otto Attolini,Susana Llanos,Sandra Pérez Ramos,Marta Escorihuela,Fatima Al-Shahrour,Timothy P. Cash,Tamara Tchkonia,James L. Kirkland,Joaquín Arribas,Manuel Serrano +18 more
TL;DR: In this article , an unbiased proteomics approach was used to identify surface markers contributing to senescent cells immune evasion and the immune checkpoint inhibitor PD-L2 was found to upregulated across multiple senescent human and murine cells.
Journal ArticleDOI
Ten challenges for clinical translation in psychiatric genetics
TL;DR: Ten challenges facing translation of psychiatric genetic findings into clinical practice are outlined, focused on the robust and generalizable detection of genetic risk factors, improved definition and assessment of psychopathology and achieving better clinical indicators.
Journal ArticleDOI
TP53-Deficient Angiosarcoma Expression Profiling in Rat Model
Urszula Smyczynska,Damian Strzemecki,Anna M. Czarnecka,Wojciech Fendler,Michal Fiedorowicz,Marlena Wełniak-Kamińska,Magdalena Guzowska,Kamil Synoradzki,Łukasz Cheda,Zbigniew Rogulski,Paweł Grieb +10 more
TL;DR: It is demonstrated that the type of developing sarcoma depends on genetic background, underscoring the importance of developing more malignancy susceptibility models in various strains and species to simulate the study of the diverse genetics of human sarcomas.
Journal ArticleDOI
Drug repositioning based on network-specific core genes identifies potential drugs for the treatment of autism spectrum disorder in children.
Huan Gao,Yuan Ni,Xueying Mo,Dantong Li,Shan Teng,Qingsheng Huang,Shuai Huang,Guangjian Liu,Sheng Zhang,Yaping Tang,Long Lu,Long Lu,Huiying Liang +12 more
TL;DR: In this paper, a network-based core gene identification method was proposed to identify the pathogenic genes of ASD, and two proposed drug repositioning methods were evaluated using gene network analysis.
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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