differential_signaling_exercises
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differential_signaling_exercises [2016/02/25 11:49] mhidalgo |
differential_signaling_exercises [2020/04/03 20:18] (current) |
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| * Experimental design: {{:GSE51835-Exercise_ED.txt|}} | * Experimental design: {{:GSE51835-Exercise_ED.txt|}} | ||
| - | **1.1.-** Run the Differential signaling tool with these files, selecting the option //Color nodes by differential expression//. Take a llok to the results. Which pathways are differentially activated? | + | **1.1.-** Run the Differential signaling tool with these files. Take a look to the results. Which pathways are differentially activated? |
| **1.2.-** What is the role of the differentially expressed genes in the pathways? | **1.2.-** What is the role of the differentially expressed genes in the pathways? | ||
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| - | **1.3.-** Run the Differential signaling tool with these files again, selecting the option //Decompose paths//. Which diferences can you find between the two methods? | ||
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| Run the Differential signaling tool with these files, selecting the options of both functional analysis //Gene ontology// and //Uniprot keywords//. | Run the Differential signaling tool with these files, selecting the options of both functional analysis //Gene ontology// and //Uniprot keywords//. | ||
| - | Try to identify representative functions of this experiment (related to the disease). Are there significative functions? Are they related with the disease? | + | **2.1.-** Try to identify representative functions of this experiment (related to the disease). Are there significative functions? Are they related with the disease? |
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| + | **2.2.-** Look at the Heatmaps provided by the tool for the different analyses. Do you think that a predictor could be trained from these data? With which matrix do you think that it would work better? | ||
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| * Experimental design: {{:kirc_demo_ED_class.txt|}} | * Experimental design: {{:kirc_demo_ED_class.txt|}} | ||
| - | **3.1.-** Run the Differential signaling tool with these files, selecting also the functional analyses. You can select the option //Color nodes by differentail expression// if desired. Look at the results. If you have done Exercises 1 or 2, can you find any difference in the results of this dataset? | + | **3.1.-** Run the Differential signaling tool with these files, selecting also the functional analyses. Find representative paths and functions of this disease. |
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| - | **3.2.-** Look at the Heatmaps provided by the tool for the different analyses. Do you think that a predictor could be trained from these data? With which matrix do you think that it would work better? | + | |
| + | **3.2.-** Look at the results. If you have done Exercises 1 or 2, can you find any difference in the results of this dataset? | ||
differential_signaling_exercises.1456400959.txt.gz · Last modified: 2020/04/03 20:17 (external edit)
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