Expression Data Visualization tool

Hiba Benaribi
Anmol Kiran
Mengyuan Ding
Elisabetta Iavarone

Tutorial developed during the SPARC Fair Codeathon 2022

Updated on May 10, 2023 (Version 1)

Corresponding Contributor:

Elisabetta Iavarone
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Dataset Overview

Study Purpose: At present, the platform SPARC Portal has no data processing or visualization system for transcriptomic and genetic data analysis purposes. So, we developed a gene expression data visualization oSPARC template. This project was developed during the 2022 SPARC FAIR Codeathon. More detailed information about the project is available here.

Data Collection: Processed transcriptomics data were imported from the SPARC Portal. In this study, we developed an o²S²PARC template to instantiate an interactive pipeline for gene expression data visualization, ontological mapping, and statistical evaluation. To demonstrate the tool's usefulness, we performed a case study on a publicly available dataset.

Primary Conclusion: The tool enables users to identify the differentially expressed genes (DEGs) and visualize them in a volcano plot format. Ontologies associated with the DEGs are assigned and visualized in barplots.

Curator's Notes

Experimental Design: This is the computational dataset. The oSPARC template can be used to visualize genes expression data from processed csv files. Two options are provided: the first is for one dataset, it generates a volcano plot, tables, and ontology graphs; and the second option is to compare two datasets of data, it provides Venn diagrams and tables.

Completeness: This dataset is complete.

Subjects & Samples: This is a computational dataset; thus no subjects are described.

Primary vs derivative data: Not applicable. This is a computational study. Only a configuration file to view and run the simulation on the oSPARC platform is provided.

Code Availability: Source code available from:


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Publishing history

May 10, 2023
Originally Published
May 10, 2023 (Version 1)
Last Updated

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