The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations - PubMed (original) (raw)

Review

. 2018 Jan 24;6(1):13-24.

doi: 10.1016/j.cels.2017.11.001. Epub 2017 Nov 29.

Sherry L Jenkins 1, Kathleen M Jagodnik 1, Simon Koplev 1, Edward He 1, Denis Torre 1, Zichen Wang 1, Anders B Dohlman 1, Moshe C Silverstein 1, Alexander Lachmann 1, Maxim V Kuleshov 1, Avi Ma'ayan 2, Vasileios Stathias 3, Raymond Terryn 3, Daniel Cooper 3, Michele Forlin 3, Amar Koleti 3, Dusica Vidovic 3, Caty Chung 3, Stephan C Schürer 3, Jouzas Vasiliauskas 4, Marcin Pilarczyk 4, Behrouz Shamsaei 4, Mehdi Fazel 4, Yan Ren 4, Wen Niu 4, Nicholas A Clark 4, Shana White 4, Naim Mahi 4, Lixia Zhang 4, Michal Kouril 4, John F Reichard 4, Siva Sivaganesan 4, Mario Medvedovic 4, Jaroslaw Meller 4, Rick J Koch 5, Marc R Birtwistle 5, Ravi Iyengar 5, Eric A Sobie 5, Evren U Azeloglu 5, Julia Kaye 6, Jeannette Osterloh 6, Kelly Haston 6, Jaslin Kalra 6, Steve Finkbiener 6, Jonathan Li 7, Pamela Milani 7, Miriam Adam 7, Renan Escalante-Chong 7, Karen Sachs 7, Alex Lenail 7, Divya Ramamoorthy 7, Ernest Fraenkel 7, Gavin Daigle 8, Uzma Hussain 8, Alyssa Coye 8, Jeffrey Rothstein 8, Dhruv Sareen 9, Loren Ornelas 9, Maria Banuelos 9, Berhan Mandefro 9, Ritchie Ho 9, Clive N Svendsen 9, Ryan G Lim 10, Jennifer Stocksdale 10, Malcolm S Casale 10, Terri G Thompson 10, Jie Wu 10, Leslie M Thompson 10, Victoria Dardov 9, Vidya Venkatraman 9, Andrea Matlock 9, Jennifer E Van Eyk 9, Jacob D Jaffe 11, Malvina Papanastasiou 11, Aravind Subramanian 12, Todd R Golub 13, Sean D Erickson 14, Mohammad Fallahi-Sichani 14, Marc Hafner 14, Nathanael S Gray 14, Jia-Ren Lin 14, Caitlin E Mills 14, Jeremy L Muhlich 14, Mario Niepel 14, Caroline E Shamu 14, Elizabeth H Williams 14, David Wrobel 14, Peter K Sorger 14, Laura M Heiser 15, Joe W Gray 15, James E Korkola 15, Gordon B Mills 16, Mark LaBarge 17, Heidi S Feiler 15, Mark A Dane 15, Elmar Bucher 15, Michel Nederlof 18, Damir Sudar 18, Sean Gross 15, David F Kilburn 15, Rebecca Smith 15, Kaylyn Devlin 15, Ron Margolis 19, Leslie Derr 19, Albert Lee 19, Ajay Pillai 19

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Review

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

Alexandra B Keenan et al. Cell Syst. 2018.

Abstract

The Library of Integrated Network-Based Cellular Signatures (LINCS) is an NIH Common Fund program that catalogs how human cells globally respond to chemical, genetic, and disease perturbations. Resources generated by LINCS include experimental and computational methods, visualization tools, molecular and imaging data, and signatures. By assembling an integrated picture of the range of responses of human cells exposed to many perturbations, the LINCS program aims to better understand human disease and to advance the development of new therapies. Perturbations under study include drugs, genetic perturbations, tissue micro-environments, antibodies, and disease-causing mutations. Responses to perturbations are measured by transcript profiling, mass spectrometry, cell imaging, and biochemical methods, among other assays. The LINCS program focuses on cellular physiology shared among tissues and cell types relevant to an array of diseases, including cancer, heart disease, and neurodegenerative disorders. This Perspective describes LINCS technologies, datasets, tools, and approaches to data accessibility and reusability.

Keywords: BD2K; L1000; MCF10A; MEMA; P100; data integration; lincsprogram; lincsproject; systems biology; systems pharmacology.

Copyright © 2017 Elsevier Inc. All rights reserved.

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Figures

Fig. 1

Fig. 1

An overview of the multi-institutional LINCS program.

Fig. 2

Fig. 2. An overview of the LINCS centers, assays, tools and platforms (not all tools are listed)

Acronyms: MEMA- microenvironment microarrays; CycIF- cyclic immunofluorescence; MS- mass spectrometry; RPPA- reverse phase protein array; GCP- global chromatin profiling; ATAC- assay for transposase accessible chromatin; OMERO- open microscopy environment; CLUE- CMap and LINCS unified environment; GR- growth response.

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