Please use this identifier to cite or link to this item: https://hdl.handle.net/11147/12585
Title: PlaqView 2.0: A comprehensive web portal for cardiovascular single-cell genomics
Authors: Ma, Wei Feng
Turner, Adam W.
Gancayco, Christina
Wong, Doris
Song, Yipei
Mosquera, Jose Verdezoto
Auguste, Gaëlle
Hodonsky, Chani J.
Prabhakar, Ajay
Ekiz, Hüseyin Atakan
van der Laan, Sander W.
Miller, Clint L.
Keywords: Cardiovascular disease
Genomics
scRNA-seq
PlaqView 2.0
Web portal
Issue Date: Aug-2022
Publisher: Frontiers Media S.A.
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 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.
Description: 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).
URI: https://doi.org/10.3389/fcvm.2022.969421
https://hdl.handle.net/11147/12585
Appears in Collections:Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

Files in This Item:
File Description SizeFormat 
fcvm-09-969421.pdfArticle (Makale)5.32 MBAdobe PDFView/Open
Show full item record



CORE Recommender

SCOPUSTM   
Citations

6
checked on Feb 17, 2024

WEB OF SCIENCETM
Citations

3
checked on Jan 27, 2024

Page view(s)

128
checked on Feb 26, 2024

Download(s)

44
checked on Feb 26, 2024

Google ScholarTM

Check




Altmetric


Items in GCRIS Repository are protected by copyright, with all rights reserved, unless otherwise indicated.