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Upload User Defined Data
There are four different formats for user-defined data listed below.
(Note: \t is the "tab" button on your keyboard)
| Description | Examples | Real Examples |
| Simplest format: a list of interacting pairs | geneA \t geneB geneB \t geneC ... |
par-1\t par-3 Y66A7A.4\tY65B4BL.5 ... |
| List of pairs, with defined data types | geneA \t geneB \t
Type1 geneB \t geneB \t Type2 ... |
par-1\t par-3\t
GI Y66A7A.4\t Y65B4BL.5\t GI ... |
| Pairs with defined data types and numerical values * | geneA \t geneB \t
Type1 \t 0.98865 geneB \t geneC \t Type2 \t 0.1 ... |
par-1\t par-3\tGI\t
0.98865 Y66A7A.4\t Y65B4BL.5\tGI\t 0.1 ... |
| Pairs with defined data types, multiple data sets, and numerical values * | geneA \t geneB \t
Type1 \t DataSet1 \t 0.83973
geneA \t geneB \t Type1 \t DataSet2 \t 0.8 ... |
par-1\t par-3\tGI\tWS150\t0.98865
Y66A7A.4\t Y65B4BL.5\tGI\tWS150\t0.1 ... |
* Numerical values may represent confidence or quality scores, correlation coefficients, or other numerical attributes.
Tip: These formats can be
generated by Microsoft Excel or OpenOffice Calc. To export data in this
format, place the data in different columns and then save as a "tab
delimited" file. (Data in each column can include spaces, but should
not include the "tab" character.) Demo
file (Right-click the hyperlink and choose "Save Target as" .csv
file)
Note: Cytoscape SIF files can be uploaded. More information
can be found here: Cytoscape
User
Manual/Network
Formats
Merging Uploaded User Defined Data
With Database
To merge your file with the database, select the Coordinate with DB
checkbox (default) and enter a starting point to query.
Multiple genes separated by a space, comma, or semi-colon can be
entered as starting points.
To keep your edge types separate when merging with the database, select
the Use custom edge types checkbox (default).
A User_ prefix will be added to the names of the edge types and
existing data sets when using the Use custom edge types checkbox.
When the Use custom edge types checkbox is not selected, the User_
prefix will only be added to edge types and data sets not found in the
database.
If data sets are not specified in the file and an edge is considered
user-defined or not found in the database (User_ prefix is
used), the default dataset name Unknown is used.