Protein ANalysis THrough Evolutionary Relationships (PANTHER) is a publicly available online tool that allows the annotation and classification of gene lists. The website is slightly less user-friendly in terms of navigation, but certainly aids in the understanding of your gene list. Users can perform functional classification, statistical over-representation, or statistical enrichment analyses on their gene lists.
Running Panther
-
1) The home page takes you straight to the Gene List Analysis tab. From here, paste your gene list into the Enter IDs box, or upload your gene list by clicking the Upload IDs link. Then ensure that ID List is selected in the Select List Type section.
-
2) Select which organism you are working with in the box.
-
3) Now select the type of anlaysis you would like to perform. To perform the analysis, select submit at the bottom of the page. I would suggest starting with the Functional classification viewed in graphic charts as either a Bar chart or Pie chart. If we proceed with the aforementioned (selecting the Bar chart option), this loads a new page with your results. At the top of the page, in the Features section, are brief instructions on how to navigate the results. Users can change the ontology of their results by using the drop-down menu above the bar chart (Select Ontology). Users can also switch between bar chart and pie chart by selecting either Bar Chart or Pie Chart above the Features section.
Statistical over-representation test To perform this test, firstly select Statistical overrepresentation test. A drop-down box will appear which requires you to select which annotation set you would like to run. Once you have chosen an annotation set, select submit. This will load a new page which asks you to select a reference list. Users can either provide their own background list or use a default whole-genome list (reccomended) by using the drop-down box on the right hand side of the page. A new page will load with an overview of the analysis you are wanting to perform. Here you have the opportunity to change the annotation data set, test type, and correction method. To perform the analysis, select Launch analysis at the bottom of the page. This will produce a table of results at the bottom of the page.
Statistical enrichment test To perform this analysis, the user must upload their gene list with an associated expression value. Once you have uploaded your file, select statistical enrichment test. Select the annotation set you want to run against in the drop-down menu and then select submit. A new page will load with a table of your results. You can easily run your gene list against other annotation sets by selecting them in the drop-down menu at the top of the page and then selecting Launch analysis.