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--- differential_signaling_exercises [2016/02/24 16:38] – mhidalgo
+++ differential_signaling_exercises [2018/12/26 21:08] (current) – krian
@@ Line 7: / Line 7: @@
 ==== Exercise 1 ====
-We will analyze a dataset with samples of healthy people (22-30 years old) before and after performing moderate exercise. This dataset has been download from the GEO database. Further information on the study can be found at [[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GDE51835]].
+We will analyze a dataset with samples of healthy people (22-30 years old) before and after performing moderate exercise. This dataset has been download from the GEO database. Further information on the study can be found at [[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GDE51835|this site]].
 You can download the expression matrix and the experimental design from the following links:
@@ Line 14: / Line 14: @@
   * 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?
-**1.3.-** Run the Differential signaling tool with these files again, selecting the option //Decompose paths//. Which diferences can you find between the two methods?
@@ Line 33: / Line 31: @@
 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 45: @@
   * 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.
-**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?
-Stages describe the natural evolution of any cancer. You can find further information on the matter in
+==== Exercise 4 ====
-[[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:
+We will work with a Breast Cancer dataset from the repository The Cancer Genome Atlas.
+There are different subtypes of Breast Cancer. In this exercise we will compare two kinds of breast cancer subtypes.
-  * Expression matrix: {{:kirc_demo_genes_vals_tumor.txt|}}
+First we will analyze the basal subtype, also called triple negative, with healthy breast tissue.
-  * Experimental design: {{:kirc_demo_ED_stages.txt|}}
+You can download the normalized expression matrix and the experimental design from these links:
-**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?
+  * Expression matrix: {{:brca_genes_vals_bn.txt|}}
+  * Experimental design: {{:brca_normal-basal_ed.txt|}}
-**3.4.-** Look for some paths which are related with disease but not with its progression.
+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:
-==== Exercise 4 ====
+  * Expression matrix: {{:brca_genes_vals_ln.txt|}}
+  * Experimental design: {{:brca_luminal-normal_ed.txt|}}
-We will work with a Breast Cancer dataset from the repository The Cancer Genome Atlas. You can download the expression matrix and the experimental design from these links:
+Identify paths and functions which are significant for each type of breast cancer.
+Try to find differences between these two subtypes of breast cancer.
-  * Expression matrix: {{:brca_genes_vals_bn.txt|}}
+If you are familiar with R, you can compare both cancer subtypes by combining both datasets and run the resulting dataset in HiPathia.
-  * Experimental design: {{:brca_normal-basal_ed.txt|}}