PlaqView 2.0: A comprehensive web portal for cardiovascular single-cell genomics
Ma, Wei Feng; Turner, Adam W; Gancayco, Christina; Wong, Doris; Song, Yipei; Mosquera, Jose Verdezoto; Auguste, Gaëlle; Hodonsky, Chani J; Prabhakar, Ajay; Ekiz, H Atakan; van der Laan, Sander W; Miller, Clint L
(2022) Frontiers in cardiovascular medicine, volume 9
(Article)
Abstract
Single-cell RNA-seq (scRNA-seq) is a powerful genomics technology to interrogate the cellular composition and behaviors of complex systems. While the number of scRNA-seq datasets and available computational analysis tools have grown exponentially, there are limited systematic data sharing strategies to allow rapid exploration and re-analysis of single-cell datasets, particularly in
... read more
the cardiovascular field. We previously introduced PlaqView, an open-source web portal for the exploration and analysis of published atherosclerosis single-cell datasets. Now, we introduce PlaqView 2.0 (www.plaqview.com), which provides expanded features and functionalities as well as additional cardiovascular single-cell datasets. We showcase improved PlaqView functionality, backend data processing, user-interface, and capacity. PlaqView brings new or improved tools to explore scRNA-seq data, including gene query, metadata browser, cell identity prediction, ad hoc RNA-trajectory analysis, and drug-gene interaction prediction. PlaqView serves as one of the largest central repositories for cardiovascular single-cell datasets, which now includes data from human aortic aneurysm, gene-specific mouse knockouts, and healthy references. PlaqView 2.0 brings advanced tools and high-performance computing directly to users without the need for any programming knowledge. Lastly, we outline steps to generalize and repurpose PlaqView's framework for single-cell datasets from other fields.
show less
Download/Full Text
Keywords: cardiovascular, database, genomics, scRNA-seq, single-cell, web portal, Cardiology and Cardiovascular Medicine
ISSN: 2297-055X
Publisher: Frontiers Media S. A.
Note: Funding Information: Funding for this research was provided by National Institutes of Health (NIH) grants R00HL125912 and R01HL14823, a Leducq Foundation Transatlantic Network of Excellence (PlaqOmics) Young Investigator Grant, Netherlands CardioVascular Research Initiative of the Netherlands Heart Foundation (CVON 2011/B019 and CVON 2017-20: Generating the best evidence-based pharmaceutical targets for atherosclerosis [GENIUS I&II]), and the ERA-CVD program druggable-MI-targets (grant number: 01KL1802). SL was funded through EU H2020 TO_AITION (grant number: 848146). Publisher Copyright: Copyright © 2022 Ma, Turner, Gancayco, Wong, Song, Mosquera, Auguste, Hodonsky, Prabhakar, Ekiz, van der Laan and Miller.
(Peer reviewed)