Steps to Follow
Data Upload Page
- Enter gene and/or protein identifiers to the text area or
upload a file with gene/protein identifiers.
Accepted gene/protein identifiers: FBgn, CG, symbol, UniProt, Entrez Gene Id. Format of data file(s):
Files can include:
- A gene list: The user can upload a file with a list of genes.
- A gene list with corresponding values: The user can upload gene-value pairs. The values for the genes can be gene expression values, z-scores, etc. The difference in the values will be represented using a color scale in the network visualization.
- An interaction list: The user can upload gene-gene pairs to indicate the interaction between them. If the same interaction is present in the database, the user will be able to see the edges between the gene-gene pairs she/he uploads. If the interaction is not present in the database, the user will see the genes in the visualization, but the genes will not be connected with an edge.
Format Example File 1 Example File 2 A gene list Single text file with one data column Excel file, single sheet with one data column A gene list with corresponding values Tab-separated values, single file with two data columns Excel file, single sheet with two data columns An interaction list Tab-separated values, single file with two data columns Excel file, single sheet with two data columns - Specify the input type ("Gene/Protein List" or "Interaction List").
- Specify the network to use ("PPI" or "STRING").
Result Page
The result page includes two main parts; network visualization and protein-protein interaction (PPI) information.
1- 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. If the input includes values for the genes, nodes will have different colors depending on the values. The color scale changes between blue to red. If the user input consists of only gene/protein names, all of the nodes in the network visualization will have the same color.
- Edges: Protein-protein interactions (PPI) are visualized by using edges. The edges can have two different colors depending on the sign of the interaction. If the sign is "-", the edge color is red and if the sign is "+", the edge color is blue.
- 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,
- click on the edge of interest to see detailed information about the protein-protein interaction,
- right click on the screen to save the network image or export it to Cytoscape.
2- Protein-Protein Interaction Information:
The user will see detailed information about protein-protein interactions
(PPI) by clicking on the edges. When clicked on an edge, the PPI information
will appear on the right side of the page.
This part consists of four different parts;
Edge:The information listed under "Edge" part are listed below.
- The sign of the edge,
- The number of screens used for prediction,
- Source type of the interaction (literature or predicted),
- Link(s) for the source (if the source is literature),
- The confidence score for sign prediction.
Screen Phenotypes: This part includes the phenotype matrix which provides information about the genetic screens used to make the prediction.
List of RNAi Screens Used to Construct the Phenotypic Matrix.
Color-coding of the Phenotype Matrix
| Color_1 | Color_2 | Correlation | |
|---|---|---|---|
| Scenario 1: | Red (Negative) | Red (Negative) | Positive Correlation |
| Scenario 2: | Red (Negative) | Blue (Positive) | Negative Correlation |
| Scenario 3: | Blue (Positive) | Blue (Positive) | Positive Correlation |
| Scenario 4: | Blue (Positive) | Red (Negative) | Negative Correlation |
Protein-Protein Interaction (PPI) Information: The information listed under this part are listed below.
- Pubmed identifier(s) and link(s) to Pubmed are listed at this part as "PPI Publication",
- Ontology term identifier(s) and link(s) to EBI Ontology Lookup Service (OLC) listed under "Approach for PPI",
- If present the interlog organisms are listed under "Interlogs". Possible interlogs are "S. cerevisiae", "H. sapiens", "M. musculus", "C. elegans" and "D. rerio".
Expression Correlation (PCC): The gene expression correlation data for Drosophila developmental time-course are derived from modENCODE database, and listed here.