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RESEARCH ARTICLE (Open Access)
Contents Vol 36(13)

ShinySperm: navigating the sperm proteome landscape

David A. Skerrett-Byrne https://orcid.org/0000-0002-1804-1826 A B C D * , Raffaele Teperino https://orcid.org/0000-0001-8815-1409 C D and Brett Nixon https://orcid.org/0000-0003-2745-8188 A B
+ Author Affiliations
- Author Affiliations

A Priority Research Centre for Reproductive Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, The University of Newcastle, Callaghan, NSW 2308, Australia.

B Infertility and Reproduction Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia.

C Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.

D German Center for Diabetes Research (DZD), Neuherberg, Germany.

* Correspondence to: David.Skerrett-Byrne@helmholtz-munich.de

Handling Editor: Ana Villaverde

Reproduction, Fertility and Development 36, RD24079 https://doi.org/10.1071/RD24079
Submitted: 28 May 2024  Accepted: 11 July 2024  Published online: 1 August 2024

© 2024 The Author(s) (or their employer(s)). Published by CSIRO Publishing. This is an open access article distributed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (CC BY-NC-ND)

Abstract

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.

Keywords: epididymis, fertility, male fertility, proteomics, publicly accessible data, ShinySperm app, sperm, sperm maturation, sperm proteome.

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