Goal: make a nice network visualization of connections between Kaplanis proteins and explore the network

1. The network shows all interactions from the IMEx dataset involving at least one Kaplanis protein -> way too many interactions. Let's focus on interactions only between Kaplanis proteins. Task: reduce network to Kaplanis proteins only and interactions between them
- Problem: which proteins are Kaplanis proteins?
- use File -> Import -> Table from file option
- select Kaplanis_285_genes_annotated.txt
- default options should be right but make sure the option "Node Table Columns" is selected. Take time to explore which other options there are, then click Ok
- this adds a column to the node table in your network with a "y" for every protein that is from the Kaplanis dataset
- go to the node table in Cytoscape and find the new Kaplanis_gene column, can you see entries with a "y"?
- if yes, proceed, if not, troubleshoot. 
- now we want to select all nodes that are not Kaplanis proteins. Use the Filter Pane for that purpose
- once you selected all non-Kaplanis genes, use the Edit Menu and select "Remove selected nodes and edges"
- what happened to your network? did it also remove all the edges that were adjacent to the selected nodes?

2. Find a nice layout of your network using the Layout Menu (one that works ok is Prefuse Force Directed OpenCL Layout), take some time to explore different layout options and think about which ones are more or less useful for your network data

3. We got still a lot of interactions, which makes it hard to prioritize proteins and interactions for further study. Let's reduce the number of interactions by retaining only interactions with good experimental evidence that these are PPIs.
- switch to the edge table and take a look at all the columns -> which ones provide information about the experimental evidence? which column should we use for the filtering and which values in that column do we want to retain? 
- use the filter option again and the edge column "Primary Interaction Type" and remove all edges from the network with "association", "proximity", or "colocalization" evidence

4. It is kind of annoying that every experimental evidence for an interaction between two proteins is shown as individual edges. Let's try to get rid of them.
- use the option "Remove duplicated edges" under the Edit Menu, select the network and both options ("ignore edge direction" and "Create an edge column...") and click Ok.
- which new edge column was created? what is its content?
- why are there still some redundant edges? what is special about them?
- use the Edit Menu, remove self-loops option to remove the remaining redundant edges

5. Among the remaining Kaplanis proteins, I would like to know whether there is also any of the newly discovered 28 developmental delay-associated proteins. How can I do this?
- use the File -> Import -> Table from file option again and the file Kaplanis_28_genes_annotated.txt. Make sure the option "Node Table Columns" is selected. Before clicking Ok take some time to explore the options again and the content of the file via the table view shown at this stage.
- once you clicked ok, try to find the new columns in the Node table. Which of these columns could be used to identify, which Kaplanis proteins are the "new" ones?

6. Let's come to the most fun part, let's display some more information on this network using the Style pane.
- once you selected the Style Pane, explore the default style options first and choose one you like.
- now, figure out how to use the style options to
- replace the proteinID with the gene name on the nodes in the network
- visualize different types of edges based on detection method
- visualize how many different pieces of experimental evidence existed for a given edge
- in case you see weird labels for edges, too, figure out how to remove them with the style options
- visualize which proteins are the "new" Kaplanis proteins
- save this modified style by copying it and giving it a name

7. To not lose all your work, save this cytoscape session as a .cys file and play with options to save the network as an image as well.

8. Time to explore your network. 
- play with how you can select nodes and edges in the network and check what happens to the node and edge table. - is there anything interesting you can observe in the network? Any interaction or protein that attracts your attention?
- which information do you miss to further explore the network for developmental delay-related interesting candidate proteins and interactions?