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

Amar Koleti, Raymond Terryn, Vasileios Stathias, Caty Chung, Daniel J. Cooper, John P. Turner, Dušica VidoviÄ ‡, Michele Forlin, Tanya T. Kelley, Alessandro D'Urso, Bryce K. Allen, Denis Torre, Kathleen M. Jagodnik, Lily Wang, Sherry L. Jenkins, Christopher Mader, Wen Niu, Mehdi Fazel, Naim Mahi, Marcin PilarczykNicholas Clark, Behrouz Shamsaei, Jarek Meller, Juozas Vasiliauskas, John Reichard, Mario Medvedovic, Avi Ma'Ayan, Ajay Pillai, Stephan C Schuerer

Research output: Contribution to journalArticle

29 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)D558-D566
JournalNucleic Acids Research
Volume46
Issue numberD1
DOIs
StatePublished - Jan 1 2018

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Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program : Integrated access to diverse large-scale cellular perturbation response data. / Koleti, Amar; Terryn, Raymond; Stathias, Vasileios; Chung, Caty; Cooper, Daniel J.; Turner, John P.; VidoviÄ ‡, Dušica; Forlin, Michele; Kelley, Tanya T.; D'Urso, Alessandro; Allen, Bryce K.; Torre, Denis; Jagodnik, Kathleen M.; Wang, Lily; Jenkins, Sherry L.; Mader, Christopher; Niu, Wen; Fazel, Mehdi; Mahi, Naim; Pilarczyk, Marcin; Clark, Nicholas; Shamsaei, Behrouz; Meller, Jarek; Vasiliauskas, Juozas; Reichard, John; Medvedovic, Mario; Ma'Ayan, Avi; Pillai, Ajay; Schuerer, Stephan C.

In: Nucleic Acids Research, Vol. 46, No. D1, 01.01.2018, p. D558-D566.

Research output: Contribution to journalArticle

Koleti, A, Terryn, R, Stathias, V, Chung, C, Cooper, DJ, Turner, JP, VidoviÄ ‡, D, Forlin, M, Kelley, TT, D'Urso, A, Allen, BK, Torre, D, Jagodnik, KM, Wang, L, Jenkins, SL, Mader, C, Niu, W, Fazel, M, Mahi, N, Pilarczyk, M, Clark, N, Shamsaei, B, Meller, J, Vasiliauskas, J, Reichard, J, Medvedovic, M, Ma'Ayan, A, Pillai, A & Schuerer, SC 2018, 'Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: Integrated access to diverse large-scale cellular perturbation response data', Nucleic Acids Research, vol. 46, no. D1, pp. D558-D566. https://doi.org/10.1093/nar/gkx1063
Koleti, Amar ; Terryn, Raymond ; Stathias, Vasileios ; Chung, Caty ; Cooper, Daniel J. ; Turner, John P. ; VidoviÄ ‡, Dušica ; Forlin, Michele ; Kelley, Tanya T. ; D'Urso, Alessandro ; Allen, Bryce K. ; Torre, Denis ; Jagodnik, Kathleen M. ; Wang, Lily ; Jenkins, Sherry L. ; Mader, Christopher ; Niu, Wen ; Fazel, Mehdi ; Mahi, Naim ; Pilarczyk, Marcin ; Clark, Nicholas ; Shamsaei, Behrouz ; Meller, Jarek ; Vasiliauskas, Juozas ; Reichard, John ; Medvedovic, Mario ; Ma'Ayan, Avi ; Pillai, Ajay ; Schuerer, Stephan C. / Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program : Integrated access to diverse large-scale cellular perturbation response data. In: Nucleic Acids Research. 2018 ; Vol. 46, No. D1. pp. D558-D566.
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AU - Cooper, Daniel J.

AU - Turner, John P.

AU - VidoviÄ ‡, Dušica

AU - Forlin, Michele

AU - Kelley, Tanya T.

AU - D'Urso, Alessandro

AU - Allen, Bryce K.

AU - Torre, Denis

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AU - Niu, Wen

AU - Fazel, Mehdi

AU - Mahi, Naim

AU - Pilarczyk, Marcin

AU - Clark, Nicholas

AU - Shamsaei, Behrouz

AU - Meller, Jarek

AU - Vasiliauskas, Juozas

AU - Reichard, John

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