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Skerrett-Byrne, D.A. ; Teperino, R. ; Nixon, B.*

ShinySperm: Navigating the sperm proteome landscape.

Reprod. Fertil. Dev. 36:RD24079 (2024)
Verlagsversion DOI PMC
Open Access Gold (Paid Option)
Creative Commons Lizenzvertrag
Context Integrated omics studies hold a crucial role in improving our understanding of reproductive biology. However, the complex datasets so generated are often only accessible via supplementary data files, which lack the capacity for interactive features to allow users to readily interrogate and visualise data of interest. Aims The intent of this technical note was to develop an interactive web-based application that enables detailed interrogation of a representative sperm proteome, facilitating a deeper understanding of the proteins identified, their relative abundance, classifications, functions, and associated phenotypes. Methods We developed a Shiny web application, ShinySperm (https://reproproteomics.shinyapps.io/ShinySperm/ ), utilising R and several complementary libraries for data manipulation (dplyr), interactive tables (DT), and visualisation (ggplot2, plotly). ShinySperm features a responsive user interface, dynamic filtering options, interactive charts, and data export capabilities. Key results ShinySperm allows users to interactively search, filter, and visualise sperm proteomics data based on key features (e.g. protein classification, sperm cell domain, presence, or absence at different maturation stages). This application responds live to filtering options and enables the generation of interactive plots and tables, thus enhancing user engagement and understanding of the data. Conclusions ShinySperm provides a robust platform for the dynamic exploration of epididymal sperm proteome data. It significantly improves accessibility and interpretability of complex datasets, allowing for effective data-driven insights. Implications This technical note highlights the potential of interactive web applications in reproductive biology and provides a plug and play script for the field to produce applications for meaningful researcher interaction with complex omic datasets.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter epididymis; fertility; male fertility; proteomics; publicly accessible data; ShinySperm app; sperm; sperm maturation; sperm proteome; Spermatozoa; Maturation
ISSN (print) / ISBN 1031-3613
e-ISSN 1031-3613
Zeitschrift Reproduction, Fertility and Development
Quellenangaben Band: 36, Heft: 13, Seiten: , Artikelnummer: RD24079 Supplement: ,
Verlag CSIRO PUBLISHING
Verlagsort Unipark, Bldg 1, Level 1, 195 Wellington Rd, Locked Bag 10, Clayton, Vic 3168, Australia
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Experimental Genetics (IEG)
Förderungen NHMRC Emerging Leadership Fellowship
National Health and Medical Research Council (NHMRC) Ideas