In bioinformatics pathway enrichment analysis is a powerful method that enables researchers to gain insights into biological pathways associated with large protein or gene sets. Whenever high throughput technologies like RNA sequencing and proteomics are used, the resulting data is in the form of a list of genes or proteins that are expressed or mutated. Pathway enrichment analysis interprets these gene lists by identifying the over-represented biological pathways. Here we will discuss various steps of using a tool called SHINYGO which is commonly used to perform Pathway enrichment analysis.
What is SHINYGO?
SHINYGO (Shiny Gene Ontology) is a web-based interactive tool designed for pathway and functional analysis. It was developed using the R Shiny framework by Dr. Ge Lab at the University of Connecticut. SHINYGO is a freely available tool and it does not require any installation or programming knowledge which makes it user-friendly. Not only that SHINYGO support various model organisms but also integrates pathway data from various sources like Reactome, KEGG, and Gene Ontology (GO) making it a highly versatile tool of Bioinformatics.
Key features:
SHINYGO’s user-friendly and easily accessible interface is ideal for researchers at all levels. This web-based software does not need any bioinformatics expertise and it rapidly generates detailed and appealing results. Furthermore, SHINYGO’s integration of several databases allows a thorough exploration of biological pathways in large gene datasets. The main key features of SHINYGO include:
· Pathway and Gene Ontology enrichment analysis
· Interactive visualization to explore relationships between enriched terms.
· Graphical visualization of results and gene characteristics.
· It supports multiple species
· Provides publication-ready network Visualization of images and tables that can be downloaded.
Steps to use SHINYGO for Pathway Enrichment Analysis:
Before using SHINYGO, you should prepare a list of genes or proteins from your experiment. The list should be in simple format listing gene symbols or IDs, it should also include the relevant species (e.g., human, mouse, and zebrafish). The list of about 100 to 2000 gene sets is encouraged to get meaningful biological insights. The steps to use SHINYGO are:
Step 01: Accessing SHINYGO
Open SHINYGO on your Web Browser, this free publicly available platform does not require any registration or installation.
Step 02: Input your Gene List
Once you are on SHINYGO main page, select the species of organism form from the dropdown list. SHINYGO supports several model organisms like human, mouse, rat and zebrafish. Now paste your list of gene symbols or IDs into the text box and make sure each gene entry is on a new line. SHINYGO can recognize many gene identifiers but for the best results stick to common formats. You can also adjust several parameters like P-value thresholds and minimum pathway size for more refined results.
Step 03: Running Analysis
Click the “submit” button to start the analysis. SHINYGO will provide data results in the form of graphs, tables, and pathway maps. The analysis may take a few seconds depending on the number of genes in your list.
Step 04: Reviewing Results
Once the analysis is complete SHINYGO will present several types of results before you, these include
1. The Pathway enrichment section will provide you a table with enriched pathways (e.g, Reactome, KEGG pathways) in your gene list along with statistical measures like P-values and fold enrichment scores which show levels of overrepresentation. Pathways with lower P-values are more enriched.
2. The Gene Ontology (GO) Enrichment section will provide GO results in three categories like biological process, molecular function, and cellular component. This will provide information about the biological or molecular process that your gene might participate in, functions at the molecular level, and cellular location where these functions are taking place.
3. Network visualization provides a network map created by SHINYGO which shows linked Gene ontology terms and enriched pathway. This graph provides a visual overview of related processes Nodes are linked based on shared genes, revealing clusters of related biological processes. This visualization assists in identifying underlying biological trends within your data.
4. The Gene Ontology (GO) Tree generated by SHINYGO allows us to explore the hierarchical relationship of enriched terms and the functional relatedness of biological categories. You can also explore deeper into categories to get terms that are relevant to your study.
5. SHINYGO provides you with pathway mapping or pathway diagrams in which your genes are highlighted. This provides us with information about the location of our desired gene in specific metabolic or signaling pathways.
Step 05: Downloading and Exporting Results
For further analysis, you can download or export your findings in different formats at SHINYGO. Download pathway and Gene Ontology tables as CSV files and save network maps and GO trees as images in formats like SVG or PNG. These high-resolution files are suitable for publishing and presenting.
Whether you are a novice or an experienced Bioinformatician by following these steps you can use SHINYGO effectively to generate valuable biological insights and explore complex biological questions.
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