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Nucleic Acids Res. 2018 Jan 4;46(D1):D558-D566. doi: 10.1093/nar/gkx1063.

Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data.

Author information

1
Center for Computational Science, University of Miami, FL, USA.
2
BD2K LINCS Data Coordination and Integration Center, Icahn School of Medicine at Mount Sinai, University of Miami, University of Cincinnati, New York NY, Miami FL, Cincinnati OH, USA.
3
Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA.
4
Department of Human Genetics and Genomics, Miller School of Medicine, University of Miami, FL, USA.
5
Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
6
Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA.
7
Division of Genome Sciences, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.

Abstract

The Library of Integrated Network-based Cellular Signatures (LINCS) program is a national consortium funded by the NIH to generate a diverse and extensive reference library of cell-based perturbation-response signatures, along with novel data analytics tools to improve our understanding of human diseases at the systems level. In contrast to other large-scale data generation efforts, LINCS Data and Signature Generation Centers (DSGCs) employ a wide range of assay technologies cataloging diverse cellular responses. Integration of, and unified access to LINCS data has therefore been particularly challenging. The Big Data to Knowledge (BD2K) LINCS Data Coordination and Integration Center (DCIC) has developed data standards specifications, data processing pipelines, and a suite of end-user software tools to integrate and annotate LINCS-generated data, to make LINCS signatures searchable and usable for different types of users. Here, we describe the LINCS Data Portal (LDP) (http://lincsportal.ccs.miami.edu/), a unified web interface to access datasets generated by the LINCS DSGCs, and its underlying database, LINCS Data Registry (LDR). LINCS data served on the LDP contains extensive metadata and curated annotations. We highlight the features of the LDP user interface that is designed to enable search, browsing, exploration, download and analysis of LINCS data and related curated content.

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