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+# 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?
+
+