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What this article shares with you is about how to understand webgestalt, an online tool for gene enrichment analysis. The editor thinks it is very practical, so I share it with you. I hope you can get something after reading this article.

In the analysis of combinatorial data, gene enrichment analysis is one of the most commonly used methods. All gene data analysis should be implemented on the function eventually. Enrichment analysis, as one of the most basic functional research methods, can explore the functions of input gene enrichment through go, kegg pathway and other different gene function annotation databases, combined with the corresponding enrichment analysis algorithm.

The necessity and importance of enrichment analysis is self-evident. There are many mature software that can carry out such analysis, such as clusterProfiler, GSEA and so on. However, the use of these tools still has a certain threshold, so it is not easy for biologists who have no programming experience to get the results of enrichment analysis through these software.

In order to facilitate the majority of researchers to carry out enrichment analysis, many online tools have been developed, which are easy to operate and easier to use. The most famous one is DAVID, which has been cited nearly 4000 times. However, the website data update is not timely, in the current view, the database version is too old, and does not support some new features annotation database.

Webgestalt is an online website that focuses on enrichment analysis, supports a variety of enrichment analysis algorithms, and covers a more comprehensive functional annotation database, which was updated in May this year.

It supports 12 species and 324 genes in ID format. Functional annotations include not only common go,kegg, but also protein-protein interactions, miRNA target genes, disease annotations, drug targets and other annotated information. Support three enrichment analysis algorithms

Overrepresentation Enrichment AnalysisORA

Gene Set Enrichment Analysis (GSEA)

Network Topology-based Analysis (NTA)

The official website provides examples of three algorithms. You can quickly grasp their usage through the sample data. No matter which enrichment algorithm is used, it is basically divided into the following two parts.

1. Basic parameters

Basic parameters specify species, enrichment analysis algorithm, corresponding functional annotation database, input gene list, background gene list and other information, as shown below

2. Advanced parameters

The advanced parameters are used to filter the output, and the corresponding parameter lists of different enrichment algorithms are slightly different. The parameters of the ORA algorithm are shown below.

Set the corresponding parameters, click the submit button directly, and submit. Different enrichment algorithms and databases show different results, but there are basic tabular data, bar charts, GSEA enrichment pictures and other results. Several common results are shown below.

1. Tables for enrichment analysis

two。 Histogram of enrichment analysis

3. GSEA enrichment analysis result chart

4. GO DAG directed acyclic graph

Webgestalt can easily achieve a variety of enrichment analysis through the click of the mouse, and the database is updated in a very timely manner. If enrichment analysis is needed, the website is definitely worth recommending and using.

The above is how to understand webgestalt, an online tool for gene enrichment analysis. The editor believes that there are some knowledge points that we may see or use in our daily work. I hope you can learn more from this article. For more details, please follow the industry information channel.

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