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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A network-based computational and experimental framework for repurposing compounds toward the treatment of non-alcoholic fatty liver disease
Danae Zareifi,Odysseas Chaliotis,Nafsika Chala,Nikos Meimetis,Maria Sofotasiou,Konstantinos Zeakis,Eirini Pantiora,Antonis Vezakis,George K. Matsopoulos,Georgios P. Fragulidis,Leonidas G. Alexopoulos +10 more
TL;DR: In this paper , a drug repositioning approach that combines in vitro steatosis models with a network-based computational platform, constructed upon genomic data from diseased liver biopsies and compound-treated cell lines, is proposed effectively repositioned therapeutic compounds.
Journal ArticleDOI
The potential of a data centred approach & knowledge graph data representation in chemical safety and drug design
TL;DR: Knowledge Graphs (KG) as mentioned in this paper are a solution to a data-centred analysis approach for drug and chemical development and safety assessment, allowing them to be used from simple data retrieval, over meta-analysis to complex predictive and knowledge discovery systems.
Journal ArticleDOI
Exploring pharmacological active ingredients of traditional Chinese medicine by pharmacotranscriptomic map in ITCM
Saisai Tian,Jingbo Zhang,Shunling Yuan,Qun-Li Wang,Chao Lv,Jin-xin Wang,Jiansong Fang,Lu Fu,Jian Yang,Xianpeng Zu,Jing Zhao,Wei Zhang +11 more
TL;DR: Wang et al. as discussed by the authors developed the largest-to-date online TCM active ingredients-based pharmacotranscriptomic platform integrated traditional Chinese medicine (ITCM) for the effective screening of active ingredients.
Posted ContentDOI
Transcriptional signatures of cell-cell interactions are dependent on cellular context
Brendan T. Innes,Gary D. Bader +1 more
TL;DR: This paper used ligand perturbation data from both the high-throughput Connectivity Map resource and published transcriptomic assays of cell lines and purified cell populations to determine whether ligand signals have unique and generalizable transcriptional signatures across biological conditions.
Journal ArticleDOI
Prognostic Ability of Enhancer RNAs in Metastasis of Non-Small Cell Lung Cancer
Jun Liu,Jin-tao Jia,Siqiao Wang,Junfang Zhang,Shuyuan Xian,Zixuan Zheng,Lin Deng,Yonghong Feng,Yuanzhi Zhang,Jie Zhang +9 more
TL;DR: This study focused on the exploration of the prognostic value of eRNAs in the metastasis of NSCLC, and six e RNAs were identified as potential markers for the prediction of metastasis.
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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