Evidence

You will want to create a seperate evidence file for each type of data that you are wanting to be used for performing infrerence. The information in these files will be used as obeserved data in order to determine the values of the rest of the cells. Where the first column name should be "gene".

The files format is a tab delimited file where the columns are the sample ids and the rows are the node ids. For DNA, RNA and protein you can use HUGO IDs. The HUGO ID will be mapped by the tool to the corresponding.

Outside of these node types you should consult the db\id\_to_name\mapping.tsv mapping file provided by Reactome. From this file you can also specify the ids for other entity types including: sets, complexes, small-molecules and generic node types. With these types you can specify them all in one file. MP-BioPath will map the specified ids to nodes that have this ID listed in on or more of the following columns: Database\_Identifier, Node\Name, Reference\_Entity_Name, and Reference_Entity_identifier. These fields are all listed in the name mapping file.

For unknown values use the number -999.