Gene enrichment analysis pipeline to analyze RNA-seq data?

Does matlab have a pipeline for gene enrichment analysis? That is, I have a list of differentially expressed genes, which I would like to analyze with the typical startegy (e.g, GO, KEGG, etc.)

[Niranjan Sundararajan]

KEGGParser: parsing and editing KEGG pathway maps in Matlab - File Exchange - MATLAB Central (mathworks.com)

does this work?

[Guy Nir]

Thanks, I'll try it out.

[Niranjan Sundararajan]

I would appreciate a thumbs up, if you found my answer helpful. Thanks!

[James Cai]

scGEAToolbox (single-cell Gene Expression Analysis Toolbox) - File Exchange - MATLAB Central

has a function for Enrichr Analysis, using MATLAB's web services capabilities to interact with Enrichr API and retrieve the results.

Answer 1

[Anshuman]

Yes, MATLAB provides tools and resources for gene enrichment analysis, allowing you to analyze lists of differentially expressed genes using various gene ontology (GO) and pathway databases such as KEGG, Reactome, and others.

1. Prepare your list of differentially expressed genes, typically represented by gene symbols or identifiers.
2. Use MATLAB's Bioinformatics Toolbox, which provides functions for accessing and retrieving gene ontology and pathway databases. For example, you can use the 'getGenes' function to retrieve gene information based on gene symbols or identifiers.
3. Utilize external resources or databases for performing gene enrichment analysis. There are several popular tools and databases available, such as DAVID, Enrichr, and clusterProfiler, which offer web-based interfaces or APIs for gene enrichment analysis.
4. You can use MATLAB's web services capabilities, such as the 'webread' function, to interact with web-based tools or APIs and retrieve the results of gene enrichment analysis.
5. Analyze and interpret the results obtained from gene enrichment analysis using MATLAB's data analysis and visualization capabilities.

Hope it helps!

[Guy Nir]

Thank you. This is along the lines of what I have been doing. Sometimes MATLAB has useful documentation with examples and entire pipelines and I feel what they have for gene enrichment analysis is a bit underwhelming.

[Wenhui Qiao]

An example to conduct 2-5 would be appreciated a lot!