Tutorial for querying analyte(s)

Querying analyte(s) of interest (Up to 3 analytes):

1: Users first needs to choose the type of network that they would like to observe

2: Enter up to 3 analytes at the same time

3: Click on the "Search" button

Network Parameter Adjustment

Network parameter can be adjusted from the box on the bottom left "Network Filters"

4: Choose the type of analytes to include in the network

5: Choose whether to include first neighbor of the neighboring nodes

6: Use the slider to adjust the number of analytes shown

7: Use the slider to significance level (NOTE: in the scale of -log10)

Specific information about the analytes and saving the figure and tables

The network figure, edge table and node table can be downloaded easily. The edge table includes connected nodes, the correlation score, type of analytes and adjusted P-Value and the node table includes analyte names and type. The downloaded files is in CSV format and can be imported to cytoscape or other software for further analysis

8: List of queried nodes

9: List of neighboring nodes. The list can be downloaded by clicking "Save Related Analytes as a CSV file"

10: More specific informations about the each analyte types, such as different ID type and link to appropriate websites

11: List of connected edges. The list can be downloaded by clicking "Save Edge as a CSV file"

Search direction

Importing edge table into Cytoscape:

If users download edge tabe as CSV file format, they can easily import them into Cytoscape.

Step 1. save edges (11) as csv file

Step 2. open Cytoscape and import csv file as network by “import network from file” menu. Please go through menu: File -> Import -> Network -> File. There you can import your CSV file. For those who do not have Cytoscape installed, please visit www.cytoscape.org

Import into cytoscape

Step 3. set up options for import network from table. If you don’t have specific request, please click OK simply.

Import option

Step 4. check visualized network from Cytoscape.

Cytoscape network

Merging integrated network and co-expression network into Cytoscape:

If users want to see different network types or combining multiple studies at once, we recommend Cytoscape for this task.

Step 1. save both network as csv files

Step 2. import networks into Cytoscape

Cytoscape networks

Step 3. merge networks by “Advanced Network Merge”. Please go through menu: Tools -> Merge -> Networks

Advanced Network Merge

After shifting networks on the list of “available networks” into “networks to merge” by clicking “>” button, users can take union or intersection of networks as they wishes.

Options for network merge

Finally, clicking “Merge” button, users can see multiple networks simultaneously like below.

Merged network