Step 1: Search interactions for a given gene/protein

1.1 start VisANT if it is not visible by clicking Start VisANT.

1.2 clear network window if it is not empty by clicking Clear button in VisANT's toolbox panel.

1.3 deselect the Auto Fit option in VisANT's toolbox's panel.

1.4 make sure the current species is Saccharomyces cerevisiae, and type in "ste4",  as shown below:

1.5 click Search button, and you will get the interactions associated with gene/protein STE4, similar to the following:

Step 2: exploratory navigation

*** Step two can be automated using macros.

2.1 double-click node YDR103W (as shown in the above image) to expand its interaction, you will get a network similar to the following:

Note: the detail of the mouse operation can be found here.

Note: interactions can also be queried by select the node, then select the menu Query Selected under Nodes menu either from menu bar, or from the pop-out menu

2.2 double-click node YDR148C (as shown in the above image) to expand its interaction, you will get a network similar to the following:

2.3 double-click node YMR072W (as shown in the above image) to expand its interaction, you will get a network similar to the following (compare the differences of the tooltip of the node YMR072W before and after double-clicking):

Similar processes can be continued until no more interactions of the interested nodes can be found.

2.4 double click node YMR072W and YDR148C, their interaction will become hidden again.

Note: the "+" symbol indicates that the node's interactions have not been expanded, while the symbol "-" indicates the interactions have been expanded.

Note: when the node has not been queried against, the tooltip of the node will show "there is ??? links", the ??? will be replaced by the actual number of the interactions once query against database is processed.

Step 3: Find the different level of neighbors for a given list of genes/proteins

3.1 clear network window if it is not empty by clicking Clear button in VisANT's toolbox panel.

3.2 select the Auto Fit option in VisANT's toolbox's panel.

3.3 change species to Homo Sapiens

3.4 type DNAJA1, RPL28 in the search box, and click the search button, you will get a network with first-level interactions of both nodes, similar to the one shown below:

3.5 do a quick layout using spring embedded relaxing layout, quickly click Stop Animation button, as shown below:

3.6 select all nodes, and query the interactions for all selected nodes, you will get an interaction network with level 2 interactions of both nodes similar to this:

3.7 click the Search button again to make both nodes to be selected

3.8 detect the shortest paths between two nodes, as shown below:

The existing shortest paths indicate that DNAJA1and RPL28 are connected, i.e., there is overlapping between their level-two interactions

Note: VisANT searches shortest paths exhaustively

Note: VisANT supports hybrid network, their shortest path from a-->b may not same as b-->a.

Step 4: Find the connections between a given set of genes/proteins

4.1 clear network window if it is not empty by clicking Clear button in VisANT's toolbox panel.

4.2 make sure current species is Homo Sapiens

4.3 copy following text in the format of edge-list into the Add box as shown in the figure below.

DNAJA1

RPL28

P53  smad4

which will add 4 nodes with P53 and smad4 being connected

4.4  make sure the 4 nodes are selected, click the menu Nodes/Query Internal Connections, a new connect between RPL28 and smad4 is displayed, as shown below: