Step 1: Upload File

You can either upload a gene list by copying and pasting the identifiers into the text box or uploading from a file. Due to the unified analysis platform of PPGR enrichment tools, it is required that the gene list file be formatted consistently, with genes separated by line breaks, where each gene occupies one line.

Gene List Demo:

Pop_A01G081890
Pop_A01G081815

Step 2: Background

If your gene list identifiers match those in PPGR, you can directly choose the species name (i.e. Populus trichocarpa). If the reference gene annotation built by PPGR does not match your identifiers, you can choose to upload a custom background file (a tab-delimited text file).

Custom Background Format Demo for KEGG :

                                        gene            KO          pathway     description
                                        Pop_A01G081890  K18835      map04626    Plant-pathogen interaction
                                        Pop_A01G081815  K08905      map00195    Photosynthesis
                                        

Step 3: Additional parameter

Threshold pvalue, usually use 0.05 or 0.01

Number of top significant pathway to be shown

Format of plot(pdf, svg, png)