diff --git a/Thursday/Thursday/OmicNet_practical.md b/Thursday/Thursday/OmicNet_practical.md new file mode 100644 index 0000000000000000000000000000000000000000..58ebf8d76890dbe5086b5fef5f0acd5ead4e4455 --- /dev/null +++ b/Thursday/Thursday/OmicNet_practical.md @@ -0,0 +1,53 @@ + +# Hands-On: OmicNet - Regulatory networks + +Here, we will explore TF - gene networks. + + +# Input: + +The gene list in the attached file contains the name of genes associated with a differential dimethylation of histone 3 (H3K4me2) in fibroblasts, upon infection with Staphylococcus. We wish to find contextual information on these genes, using known interaction networks. + +<details> + <summary markdown="span">Input data[Thursday/data/GeneList.txt]</summary> + +</details> + +OmicsNet is a web-based tool to explore multi-omics data and perform visual analysis of biological networks. It can integrate new data with of high-quality molecular interaction data, such as protein–protein interactions (PPI), gene regulatory networks. + +1. Upload the gene list in: https://www.omicsnet.ca/ and build your network defining a primary Interaction type. + +HW2-Q1: Which kind of interaction would you choose to: + +* Explore the signalling pathways where the query genes have a major role? + +* Find the transcription factors (TFs) involved in the regulation of the query genes? + + +2. For the second case, change the database used for building the network and calculate the network size, in terms of number of nodes and edges. + +HW2-Q2: Explain why are networks bigger or smaller depending on the interaction database. + + +3. Choose the interaction network for the second case, and choose the database with fewest interactions. Control the network size by trimming with the "Shortest path-based algorithm". Proceed to the network visualization. + +HW2-Q3: What is the size of the network? What are the 5 top "hubs" of your network? + +4. Identify the network modules using the different algorithms in the Module Explorer section. + +HW2-Q4: Are the different results robust among the different algorithms? Do they make sense in the light of the global network structure? How representative are the modules of the initial network? + +5. Choose the algorithm that defines the highest number of modules and perform the functional analysis of the modules with the Function Explorer. + +HW2-Q5: What are the significant pathways (alpha=0.05) that include more than 5 genes of the network? + + +6. Enlarge the network by adding edges/nodes for a given TF, using the Regulation Explorer. + +HW2-Q6: What is the biological meaning of the edges you're adding? + +7. Identify the connections between the "hubs" of two modules, using the Path Explorer. + +HW2-Q6: What are the genes involved? + +