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 Pilarczyk; Nicholas Clark; Behrouz Shamsaei; Jarek Meller; Juozas Vasiliauskas; John Reichard; Mario Medvedovic; Avi Ma'Ayan; Ajay Pillai; Stephan C. Schürer

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

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. Schürer

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135 Scopus citations

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 language	English
Pages (from-to)	D558-D566
Journal	Nucleic Acids Research
Volume	46
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkx1063
State	Published - 4 Jan 2018
Externally published	Yes

Bibliographical note

Publisher Copyright:
© 2017 The Author(s) .

Funding

1Center for Computational Science, University of Miami, FL, USA, 2BD2K 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, 3Department of Molecular and Cellular Pharmacology, Miller School of Medicine, University of Miami, FL, USA, 4Department of Human Genetics and Genomics, Miller School of Medicine, University of Miami, FL, USA, 5Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 6Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati, Cincinnati, OH, USA and 7Division of Genome Sciences, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA National Heart, Lung, and Blood Institute through funds provided by the National Institutes of Health Translational Research [U54HL127624]; Library of Integrated Network-based Cellular Signatures (LINCS) Program (http://www. lincsproject.org/); National Institutes of Health Translational Research Big Data to Knowledge (BD2K) initiative (http://www.bd2k.nih.gov/). Funding for open access charge: NIH [U54HL127624]. Conflict of interest statement. None declared.

Funders	Funder number
National Institutes of Health
National Heart, Lung, and Blood Institute	T32HL007824, U54HL127624
National Human Genome Research Institute
Human Genome Sciences
University of Miami
Office of Extramural Research, National Institutes of Health
Icahn School of Medicine at Mount Sinai
University of Cincinnati
Leonard M. Miller School of Medicine

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1093/nar/gkx1063

Cite this

Koleti, A., Terryn, R., Stathias, V., Chung, C., Cooper, D. J., Turner, J. P., VidoviÄ ‡, D., Forlin, M., Kelley, T. T., D'Urso, A., Allen, B. K., Torre, D., Jagodnik, K. M., Wang, L., Jenkins, S. L., Mader, C., Niu, W., Fazel, M., Mahi, N., ... Schürer, S. C. (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, 46(D1), D558-D566. https://doi.org/10.1093/nar/gkx1063

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

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.",

author = "Amar Koleti and Raymond Terryn and Vasileios Stathias and Caty Chung and Cooper, \{Daniel J.\} and Turner, \{John P.\} and \{Vidovi{\"A} ‡\}, Du{\v s}ica and Michele Forlin and Kelley, \{Tanya T.\} and Alessandro D'Urso and Allen, \{Bryce K.\} and Denis Torre and Jagodnik, \{Kathleen M.\} and Lily Wang and Jenkins, \{Sherry L.\} and Christopher Mader and Wen Niu and Mehdi Fazel and Naim Mahi and Marcin Pilarczyk and Nicholas Clark and Behrouz Shamsaei and Jarek Meller and Juozas Vasiliauskas and John Reichard and Mario Medvedovic and Avi Ma'Ayan and Ajay Pillai and Sch{\"u}rer, \{Stephan C.\}",

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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 & Schürer, 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

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AU - Koleti, Amar

AU - Terryn, Raymond

AU - Stathias, Vasileios

AU - Chung, Caty

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

AU - Jagodnik, Kathleen M.

AU - Wang, Lily

AU - Jenkins, Sherry L.

AU - Mader, Christopher

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

AU - Medvedovic, Mario

AU - Ma'Ayan, Avi

AU - Pillai, Ajay

AU - Schürer, Stephan C.

PY - 2018/1/4

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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

Abstract

Bibliographical note

Funding

UN SDGs

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