KEGG pathway analysis with uploaded gene list

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Prepare a list of genes

After users have uploaded a list of genes, users can first browse the expression levels of these gene in different cancer types in TACCO. Users can select a cancer type and the expression levels, fold changes and p-values for the uploaded genes in that cancer type will be listed in the table. Users can click on Go to pathway analysis.

In pathway analysis page, users can select all genes (the blue box) or select a subset of genes based on fold changes or p-values. After a gene list is specify, users can start KEGG pathway enrichment analysis by clicking on "Start".

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KEGG pathway enrichment results

TACCO provides the gene ratio distribution plot for enriched KEGG pathways. Users can download, zoom in, zoom out or reset the plot.



TACCO also provides the connected network plot for enriched KEGG pathways. Pathways sharing the same gene(s) are connected in the network plot. Users can also download, zoom in, zoom out or reset the plot.



Detailed information for KEGG enrichment analysis is listed in the table. Users can download the table or select a pathway of interest and visit KEGG website. TACCO will open a new page for users to explore the selected pathway in KEGG.



A KEGG pathway example, in which TACCO highlight all the selected genes with the red boxes.