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--- differential_signaling_exercises [2016/02/25 11:27] – mhidalgo
+++ differential_signaling_exercises [2017/05/24 14:33] (current) – external edit 127.0.0.1
@@ Line 33: / Line 33: @@
 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?
+**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?
@@ Line 45: / Line 47: @@
   * 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. You can select the option //Color nodes by differentail expression// if desired. Find representative paths and functions of this disease.
-**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?
-Stages describe the natural evolution of any cancer. You can find further information on the matter in
-[[http://www.cancer.gov/about-cancer/diagnosis-staging/staging/staging-fact-sheet]].
-Now we will try to understand how the Kidney cancer evolves by comparing the initial (I) with the final (IV) stages. We will use a subset of the former matrix, with a new experimental design, that you can download from the following links:
-  * Expression matrix: {{:kirc_demo_genes_vals_tumor.txt|}}
-  * Experimental design: {{:kirc_demo_ED_stages.txt|}}
-**3.3.-** Run the Differential signaling tool with the former files comparing stage I versus stage IV. Compare the results with those given in Exercise 3.1. Are there any differences? What do they mean?
+**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?
-**3.4.-** Look for some paths which are related with disease but not with its progression.
 ==== Exercise 4 ====
@@ Line 75: / Line 65: @@
 Then we will analyze the luminal subtype. This subtype is divided in two classes, A and B, but we will not take into account this division. You can download the normalized expression matrix and the experimental design from these links:
-  * Expression matrix: {{:brca_genes_vals_bl.txt|}}
+  * Expression matrix: {{:brca_genes_vals_ln.txt|}}
-  * Experimental design: {{:brca_normal-luminal_ed.txt|}}
+  * Experimental design: {{:brca_luminal-normal_ed.txt|}}
 Identify paths and functions which are significant for each type of breast cancer.