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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Identification of C3 as a therapeutic target for diabetic nephropathy by bioinformatics analysis.
TL;DR: Correlation analysis with GFR showed that SYK, CXCL1, LYN, VWF, ANXA1, C3, HLA-E, RHOA, SERPING1, EGF and KNG1 may be involved in diabetic nephropathy.
Journal ArticleDOI
OUP accepted manuscript
TL;DR: SigCom LINCS as mentioned in this paper is a web server that provides a rapid signature similarity search for mimickers and reversers given sets of up and down genes, a gene set, a single gene, or any search term.
Journal ArticleDOI
Epigenetic pathways and plasticity in brain tumors.
TL;DR: Some of the epigenetic pathways that have been shown to be active in three different primary brain tumors, glioblastoma (GBM), medulloblastomas (MB), and diffuse intrinsic pontine glioma (DIPG) are summarized and compared to identify common epigenetics pathways to treat in the respective cells-of-origin for these tumors.
Journal ArticleDOI
FRMD6 has tumor suppressor functions in prostate cancer.
Jakob Haldrup,Jakob Haldrup,Siri H. Strand,Siri H. Strand,Clara Cieza-Borrella,Magnus E. Jakobsson,Maria Riedel,Maibritt Nørgaard,Maibritt Nørgaard,Stine Hedensted,Stine Hedensted,Frederik Dagnæs-Hansen,Benedicte Parm Ulhøi,Rosalind A. Eeles,Michael Borre,Jesper V. Olsen,Martin K. Thomsen,Zsofia Kote-Jarai,Karina Dalsgaard Sørensen,Karina Dalsgaard Sørensen +19 more
TL;DR: FRMD6 was identified as a novel tumor suppressor gene and prognostic biomarker candidate in PC and identified pyroxamide as a new potential therapy for FRMD6 deficient PC cells.
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Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships.
Jon Sánchez-Valle,Héctor Tejero,José M. Fernández,David Juan,Beatriz Urda-García,Salvador Capella-Gutierrez,Fatima Al-Shahrour,Rafael Tabarés-Seisdedos,Anaïs Baudot,Anaïs Baudot,Anaïs Baudot,Vera Pancaldi,Vera Pancaldi,Alfonso Valencia +13 more
TL;DR: A disease interaction network inferred from similarities between patients’ molecular profiles is built, which significantly recapitulates epidemiologically documented comorbidities and discoveries in patient subgroups are discovered.
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.
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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