Cell’s favorite enrichment and analysis tools for differential genes go and KEGG

Time:2022-5-3

For transcriptome analysis, after the completion of differential gene screening, it is more than half of the success. Next, the downstream analysis can be carried out. First of all, the most common is the enrichment analysis of up and down regulated genes. We have published an R language version before:

Cluster Profiler: a surprise work of gene function enrichment analysis

We will not repeat here. We will introduce metascape, a function enrichment tool that NCS articles prefer and has a high occurrence rate(https://metascape.org/gp/index.html)。

Cell's favorite enrichment and analysis tools for differential genes go and KEGG

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Metascape is a free online tool that is easy to use and operate. More importantly, it contains multiple databases, with reliable results and good visualization results. It can be directly used to publish articles. In many articles, it is directly used to export graphs from metascape.

Cell's favorite enrichment and analysis tools for differential genes go and KEGG

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1、 Basic analysis

Next, let’s see how to operate. Step1: paste the gene name directly. Step 2: select species. Step3: click express analysis (including all results). You can wait for the result.

Cell's favorite enrichment and analysis tools for differential genes go and KEGG

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After analysis, click analysis report to view the results. Histogram containing enrichment results, which has been used to remove redundant information:

Cell's favorite enrichment and analysis tools for differential genes go and KEGG

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Pathway and Process Enrichment Analysis:

Cell's favorite enrichment and analysis tools for differential genes go and KEGG

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There are also gene interaction, transcription factors, disease database enrichment and so on. Final results click on the top of the page to download all the results, including Excel sheets, graphics and so on.

Cell's favorite enrichment and analysis tools for differential genes go and KEGG

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2、 Selective analysis

If you don’t want to select all databases at the beginning of the analysis, and only need some analysis, such as go and KEGG, select custom analysis after uploading the genes on the home page. Then you can select the corresponding database, set the threshold, and then click enrichment analysis to wait for the results.

Cell's favorite enrichment and analysis tools for differential genes go and KEGG

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3、 Multi group analysis

What I mentioned above is a group of enrichment analysis. If there are multiple groups, metascape can also be realized. To upload genes, group them, select multiple gene list, and then upload files. Then the subsequent analysis is the same as before.

Heatmap shows enrichment results:

Cell's favorite enrichment and analysis tools for differential genes go and KEGG

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Protein-protein Interaction Enrichment Analysis:

Cell's favorite enrichment and analysis tools for differential genes go and KEGG

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In short, the use of metascape is very convenient. We can also see from its home page that many articles choose to use this tool for function enrichment analysis, so don’t worry about using it!

Although the visualization results of metascape are very good, in the next section, we will talk about how to display personalized enrichment results to make our results more tall!

Previous highlights * * * *:

1、Heat map 5: ggplot2 heat map drawing and personalized decoration

2、Reproduce the chart of nature communications (II): once and for all, R language draws the expression box line diagram with one click and adds significance

3、Transcriptome non human series (III): PCA analysis and CNS level mapping

4、Transcriptome not asking for people series (10): NCS level volcano map, there is always one for you!

5、Transcriptome not asking for people series (11): drawing different Wayne diagrams in R language