Getting Started with LINCS Datasets and Tools

Zhuorui Xie; Eryk Kropiwnicki; Megan L. Wojciechowicz; Kathleen M. Jagodnik; Ingrid Shu; Allison Bailey; Daniel J.B. Clarke; Minji Jeon; John Erol Evangelista; Maxim V. Kuleshov; Alexander Lachmann; Abhijna A. Parigi; Jose M. Sanchez; Sherry L. Jenkins; Avi Ma'ayan

doi:10.1002/cpz1.487

Getting Started with LINCS Datasets and Tools

Zhuorui Xie, Eryk Kropiwnicki, Megan L. Wojciechowicz, Kathleen M. Jagodnik, Ingrid Shu, Allison Bailey, Daniel J.B. Clarke, Minji Jeon, John Erol Evangelista, Maxim V. Kuleshov, Alexander Lachmann, Abhijna A. Parigi, Jose M. Sanchez, Sherry L. Jenkins, Avi Ma'ayan

Research output: Contribution to journal › Article › peer-review

Abstract

The Library of Integrated Network-based Cellular Signatures (LINCS) was an NIH Common Fund program that aimed to expand our knowledge about human cellular responses to chemical, genetic, and microenvironment perturbations. Responses to perturbations were measured by transcriptomics, proteomics, cellular imaging, and other high content assays. The second phase of the LINCS program, which lasted 7 years, involved the engagement of six data and signature generation centers (DSGCs) and one data coordination and integration center (DCIC). The DSGCs and the DCIC developed several digital resources, including tools, databases, and workflows that aim to facilitate the use of the LINCS data and integrate this data with other publicly available data. The digital resources developed by the DSGCs and the DCIC can be used to gain new biological and pharmacological insights that can lead to the development of novel therapeutics. This protocol provides step-by-step instructions for processing the LINCS data into signatures, and utilizing the digital resources developed by the LINCS consortia for hypothesis generation and knowledge discovery.

Original language	English
Article number	e487
Journal	Current Protocols
Volume	2
Issue number	7
DOIs	https://doi.org/10.1002/cpz1.487
State	Published - Jul 2022
Externally published	Yes

Bibliographical note

Funding Information:
This work was partially supported by NIH grants OT2OD030160, U54HL127624 and OT3OD025459.

Publisher Copyright:
© 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.

Keywords

bioinformatics
disease
drug discovery
gene sets visualization
signature analysis
web application

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10.1002/cpz1.487

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title = "Getting Started with LINCS Datasets and Tools",

abstract = "The Library of Integrated Network-based Cellular Signatures (LINCS) was an NIH Common Fund program that aimed to expand our knowledge about human cellular responses to chemical, genetic, and microenvironment perturbations. Responses to perturbations were measured by transcriptomics, proteomics, cellular imaging, and other high content assays. The second phase of the LINCS program, which lasted 7 years, involved the engagement of six data and signature generation centers (DSGCs) and one data coordination and integration center (DCIC). The DSGCs and the DCIC developed several digital resources, including tools, databases, and workflows that aim to facilitate the use of the LINCS data and integrate this data with other publicly available data. The digital resources developed by the DSGCs and the DCIC can be used to gain new biological and pharmacological insights that can lead to the development of novel therapeutics. This protocol provides step-by-step instructions for processing the LINCS data into signatures, and utilizing the digital resources developed by the LINCS consortia for hypothesis generation and knowledge discovery.",

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year = "2022",

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doi = "10.1002/cpz1.487",

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Getting Started with LINCS Datasets and Tools

Abstract

Bibliographical note

Keywords

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