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_A01G081846.T1
Pop_A01G081857.T1

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 GO :

                                        gene	GO	level
                                        Pop_A01G081846.T1	GO:0005575	CC
                                        Pop_A01G081857.T1	GO:0006355	BP
                                        Pop_A01G081857.T1	GO:0007275	BP
                                        Pop_A01G081868.T1	GO:0003674	MF
                                        Pop_A01G081868.T1	GO:0005048	MF
                                        

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)