As long as the user supplies the necessary association and marker-to-gene mapping files, it is possible to conduct MSEA on data types other than human GWAS (i.e. GWAS from another species, EWAS, metabolome, etc.). MSEA is robust accross multiple species and data types. Here, we provide sample files and examples as to how MSEA can be applied to Mouse GWAS and Human EWAS data types. The output formats of these analyes are conssitent with the MSEA Example above, and thus can be utilized in the downstream wKDA Analysis.

1. To conduct MSEA on data types other than the Human GWAS Example provided above is quite simple and follows much the same procedure as the Human GWAS MSEA example. The only differences are the association files and marker-to-gene mapping files are supplied by the user.
2. Example Mouse GWAS Association files have been provided in the Association Dataset section and can be implemented as demonstrated there. These files have the marker to trait association from the mouse GWAS. The full file is also available for download at the download section.
• 

• MARKER	VALUE
  rs13459	2.202
  rs13462	1.114
  rs12463	0.939

3. Example Mouse GWAS Marker-to-Gene Mapping files have been provided in the Marker Mapping section. These files map the mouse GWAS loci to genes. The full file is also available for download in the download section.
• 
• 

• GENE	MARKER
  MACROD1	rs27240
  CTSF	rs38597
  ANXA4	rs31420

4. The Selection of Parameters is identical to those demonstrated in the MSEA Parameter Selection section of the tutorial.
5. The remainder of the MSEA pipeline for Mouse GWAS follows the same workflow as the MSEA Human GWAS Tutorial shown above, picking back up at Step 4: Gene Sets.

IMPORTANT: This methodology can be applied to Meta-MSEA. Specifically, multiple types of assocation data (i.e. GWAS from multiple species, EWAS, metabolome, etc.) can all be integrated using Meta-MSEA as long as the user provides the correct association and marker-to-gene mapping files.

1. To conduct MSEA on data types other than the Human GWAS Example provided above is quite simple and follows much the same procedure as the Human GWAS MSEA example. The only differences are the association files and marker-to-gene mapping files are supplied by the user.
2. Example Human EWAS Association files have been provided in the Association Dataset section and can be implemented as demonstrated there. These files have the marker to trait association from the human EWAS. The full file is also available for download at the download section.
• 

• MARKER	VALUE
  cg24411	0.0006
  cg10222	0.0004
  cg00962	0.0013

3. Example Human EWAS Marker-to-Gene Mapping files have been provided in the Marker Mapping section. These files map the human EWAS markers to genes. The full file is also available for download in the download section.
• 
• 

• GENE	MARKER
  A1CF	cg24411
  A1CF	cg10222
  A2BP1	cg00962

4. The Selection of Parameters is identical to those demonstrated in the MSEA Parameter Selection section of the tutorial, with the addition of one step: it is run with marker permutation.
• 
5. The remainder of the MSEA pipeline for Human EWAS follows the same workflow as the MSEA Human GWAS Tutorial shown above, picking back up at Step 4: Gene Sets.

IMPORTANT: This methodology can be applied to Meta-MSEA. Specifically, multiple types of assocation data (i.e. GWAS from multiple species, EWAS, metabolome, etc.) can all be integrated using Meta-MSEA as long as the user provides the correct association and marker-to-gene mapping files.