Steps to Follow
Data Upload Page
1- After entering the input, specify the input type ("Gene/Protein List" or "Gene/Protein List with Values" or "Interaction List").
2- Enter gene and/or protein identifiers to the text area or
upload a file containing gene-value or gene-gene pairs.
Data Format Options and Sample Data Files
DirectedPPI web tool accepts tab separated text files or Excel files.
| Format | Example Files |
|---|---|
| A gene list | File with one data column containing gene identifiers |
| A gene list with corresponding values | File with two data columns, the first column with gene identifiers and the second column with corresponding values |
| An interaction list | File with two data columns, the first column with gene identifiers and the second column with interacting gene identifiers |
Result Page
The result page includes two main parts; network visualization and node information.
Network visualization: When the user uploads a file or enters a gene list to the text area, she/he will see the visualization of the uploaded data. If the user input corresponds to any interaction in the database, the edges between the nodes will be visible.
- Nodes: Genes and/or proteins uploaded by the user are represented by the nodes in the network visualization. The nodes are labeled with the gene symbols. Nodes are represented by different colors and shapes based on their classification in the network. Indispensable nodes are shown as purple triangles, dispensable nodes are shown as turquoise circles and neutral nodes are shown as pink squares.
- Edges: Protein-protein interactions (PPI) are visualized by using edges. The direction of the interaction is represented by arrows.
Node classification:
- Indispensable: A node is defined as indispensable if its removal results in increased number of MDS (node 2 in the Figure)
- Neutral: A node is neutral if its removal has no effect on MDS (node 1 in the Figure)
- Dispensable: A node is dispensable if its removal reduces the number of MDS (node 3 and 4 in the Figure)
Color-coding of the Node Classifiaction
| Node Class | Shape | Color |
|---|---|---|
| Indispensable | Triangle | Red |
| Dispensable | Circle | Blue |
| Neutral | Square | Pink |
If the user provides gene-value pairs in a file, the color of the nodes will be in a scale from orange to green calculated based on the values from the input.
The user can
- Single click on the node of interest to see the information about the node,
- Double click on the node of interest to expand the network,
- refresh the layout by choosing one of the layout options; "Force Directed", "Compound Spring Embedder", "Circle", "Radial", and "Tree",
- change the sign prediction confidence by using the slider at the bottom of the network visualization,
- search for the gene(s) in the network visualization by entering the gene(s) of interest to the search box and choosing the "search" option,
- add gene(s) to the network visualization by entering the gene(s) of interest to the search box and choosing the "add" option,
- right click on the screen to save the network image or export it to Cytoscape.