NETWORK ANALYSIS
GO ENRICHMENT ANALYSIS
KEGG PATHWAY ANALYSIS
SIMULATION WITH JIMENA
VISUAL WITH SQUADD
Protein-Protein Interaction
Please select the organisms you want or add your protein list in as UniProtKB to the multiple protein box and choose the layout for the network to be created. If you want to add and delete Node and Edge, click the edit button. You can add nodes anywhere in the network and change the label. Click the Add Edge button to add Edge. Click on a node and drag the edge to another node to connect them.
GO Enrichment Analysis
Load your differential gene expression data or you can use example data (LUAD) and select the columns containing the Gene names and log2FC values. Choose the keytype of your genes. Set your parameters for GO Enrichment and KEGG pathway analysis. Then click the Run Analysis button.
Table
KEGG Pathway Analysis
Please be sure to select the data/parameters found in the GO enrichment tab and start the analysis. You will see your KEGG enrichment analysis results here. To see the pathway colored according to the logFC values you have given, paste an ID of your interest from the data obtained as a result of the KEGG Pathway analysis into the input pathway box. For example: hsa05212
JIMENA
Upload your signaling network data.
Your (.txt) file should contain activation/inhibition information, node1, label and node2 as column headers.
Then please click the (convert graphml) button.
Now, you can start the jimena simulation.
Perturbation setting Step 2
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SQUADD
Simulation with SQUADD Package
Please run Jimena before using the SQUADD part and identify the perturbation nodes you want to add. The data obtained as a result of Add Perturbation are used. In the tab below, the prediction heatmap and PCA circle graphics that belong to the nodes you selected are created.
Please run Jimena before using the SQUADD part and identify the perturbation nodes you want to add. The data obtained as a result of Add Perturbation are used. In the tab below, the prediction heatmap and PCA circle graphics that belong to the nodes you selected are created.