In this first major update of the portal (available at http://lincsportal.ccs.miami.edu/signatures), substantial changes in both the data architecture, and the user interface, are being introduced to enable a deeper exploration of the LINCS data, and to support new integrative and analytical capabilities for both computational and non-computational researchers. The cornerstone of this update has been the decision to reprocess all high-level LINCS datasets and make them accessible at the data-point level enabling users to directly access and download any subset of signatures across the entire library independent from the originating source, project or assay. Access to the individual signatures also enables the newly implemented signature search functionality, which utilizes the iLINCS platform to identify conditions that mimic or reverse gene set queries, and a newly designed query interface enables global metadata search with autosuggest across all annotations associated with perturbations, model systems, and signatures.
Currently in Phase 2, LINCS consists of six Data and Signature Generation Centers (DSGCs) and one Data Coordination and Integration Center (DCIC) that together have produced over 400 datasets and over 50 analytical tools focusing on the deeper understanding of complex diseases and the development of novel and effective therapies.
The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program with the goal of generating a large-scale and comprehensive catalogue of perturbation-response signatures by utilizing a diverse collection of: Perturbations (e.g. chemical, genetic, disease state), Model Systems (e.g. cell lines, differentiated cells, embryonic stem cells) and Sssay Types (e.g. gene expression, protein expression, epigenetic modification, imaging).
LINCS is a project by Dr. Stephen Schürer and his team. Read the whole update at Oxford Academic’s Nucleic Acids Research Journal (NAR).
Nucleic Acids Research ( NAR ) publishes the results of leading edge research into physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions. It enables the rapid publication of papers under the following categories: Chemistry and synthetic biology; Computational biology; Gene regulation, chromatin and epigenetics; Genome integrity, repair and replication; Genomics; Molecular biology; Nucleic acid enzymes; RNA and Structural biology. A Survey and Summary section provides a format for brief reviews. The first issue of each year is devoted to biological databases, and an issue in July is devoted to papers describing web-based software resources of value to the biological community.
CITE: Vasileios Stathias, John Turner, Amar Koleti, Dusica Vidovic, Daniel Cooper, Mehdi Fazel-Najafabadi, Marcin Pilarczyk, Raymond Terryn, Caty Chung, Afoma Umeano, Daniel J B Clarke, Alexander Lachmann, John Erol Evangelista, Avi Ma’ayan, Mario Medvedovic, Stephan C Schürer, LINCS Data Portal 2.0: next generation access point for perturbation-response signatures, Nucleic Acids Research, 11/08/2019, gkz1023, https://doi.org/10.1093/nar/gkz1023