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
Reads0
Chats0
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
More filters
Journal ArticleDOI
Prime-seq, efficient and powerful bulk RNA sequencing
Aleksandar Janjic,Lucas E. Wange,Johannes W. Bagnoli,Johanna Geuder,Phong Nguyen,Daniel Richter,Beate Vieth,Binje Vick,Irmela Jeremias,Christoph Ziegenhain,Ines Hellmann,Wolfgang Enard +11 more
TL;DR: In this paper , the authors optimize and validate prime-seq, an early barcoding bulk RNA-seq method, and show that it performs equivalently to TruSeq, but is four times more cost-efficient due to almost 50 times cheaper library costs.
Journal ArticleDOI
High-dimensional gene expression and morphology profiles of cells across 28,000 genetic and chemical perturbations
TL;DR: In this paper , the authors provide a collection of four datasets with both gene expression and morphological profile data useful for developing and testing multimodal methodologies and define biological problems that use the shared and complementary information in these two data modalities, provide baseline analysis and evaluation metrics for multi-omic applications.
Journal ArticleDOI
Hypoxic microenvironment induced spatial transcriptome changes in pancreatic cancer.
Huizhi Sun,Danfang Zhang,Chongbiao Huang,Yuhong Guo,Zhao Yang,Nan Yao,Xueyi Dong,Runfen Cheng,Nan Zhao,Jie Meng,Baocun Sun,Jihui Hao +11 more
TL;DR: In this article, spatial transcriptomics (STs) was used to investigate the ST features of engrafted human pancreatic ductal adenocarcinoma (PDAC) inthe ischemic hind limbs of nude mice.
Journal ArticleDOI
Connecting chemistry and biology through molecular descriptors
TL;DR: In this paper , a new generation of data-driven descriptors has arisen providing a rich portrait of small molecule characteristics that goes beyond chemical properties, covering chemical compounds, proteins and other biological entities, such as diseases and cell lines.
Journal ArticleDOI
TOP2A and CENPF are synergistic master regulators activated in cervical cancer
Beiwei Yu,Long Chen,Weina Zhang,Yue Li,Yibiao Zhang,Yuan Gao,Xianlin Teng,Libo Zou,Qian Wang,Hongtao Jia,Xiangtao Liu,Hui Zheng,Ping Hou,Hongyan Yu,Ying Sun,Zhiqin Zhang,Ping Zhang,Liqin Zhang +17 more
TL;DR: Two MRs, DNA topoisomerase II alpha and centromere protein F ( CENPF) were found to be up-regulated, activated and synergistic in CC compared to N across the 10 datasets, and may be good biomarkers and anticancer drug targets for CC.
References
More filters
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.
Related Papers (5)
The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity
Jordi Barretina,Giordano Caponigro,Nicolas Stransky,Kavitha Venkatesan,Adam A. Margolin,Adam A. Margolin,Sungjoon Kim,Christine D. Wilson,Joseph Lehar,Gregory V. Kryukov,Dmitriy Sonkin,Anupama Reddy,Manway Liu,Lauren Murray,Michael F. Berger,Michael F. Berger,John Monahan,Paula Morais,Jodi Meltzer,Adam Korejwa,Judit Jané-Valbuena,Judit Jané-Valbuena,Felipa A. Mapa,Joseph Thibault,Eva Bric-Furlong,Pichai Raman,Aaron Shipway,Ingo H. Engels,Jill Cheng,Guoying K. Yu,Jianjun Yu,Peter Aspesi,Melanie de Silva,Kalpana Jagtap,Michael D. Jones,Li Wang,Charlie Hatton,Emanuele Palescandolo,Supriya Gupta,Scott Mahan,Carrie Sougnez,Robert C. Onofrio,Ted Liefeld,Laura E. MacConaill,Wendy Winckler,Michael R. Reich,Nanxin Li,Jill P. Mesirov,Stacey Gabriel,Gad Getz,Kristin G. Ardlie,Vivien W. Chan,Vic E. Myer,Barbara L. Weber,Jeffrey A. Porter,Markus Warmuth,Peter Finan,Jennifer L. Harris,Matthew Meyerson,Matthew Meyerson,Todd R. Golub,Michael Morrissey,William R. Sellers,Robert Schlegel,Levi A. Garraway,Levi A. Garraway +65 more