====== Worked example Differential signaling ======
{{:youtube.png?direct&30|https://www.youtube.com/watch?v=ytyagfQpQPk&feature=youtu.be}}:https://www.youtube.com/watch?v=ytyagfQpQPk&feature=youtu.be


**1-** Log in into HiPathia. For further information on this step visit [[logging_in|Logging in]].

**2-** 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:

  * Expression matrix: {{:brca_genes_vals_bn.txt|}}
  * Experimental design: {{:brca_normal-basal_ed.txt|}}

**3-** Upload the data to HiPathia in the data panel by clicking on //My data//. For further information on this step visit [[upload_your_data|Upload your data]].

**4-** Press the //Differential signaling// button. 

{{ :hipathia_bar_diffsig_5.png?600 |}}

**5-** In the //Input data panel//. Press the //File browser// of the //Expression matrix file//, and select the desired file.

{{ :hipathia_work1.png?600 |}}

**6-** In the //Design data// panel select //Two group comparison//. Press the //File browser// of the //Experimental design file//, and select the desired file. Automatically //Condition 1// and //Condition 2// files are selected. Change //Condition 1// to "Tumor" and //Condition 2// to "Normal".

{{ :hipathia_work2.png?600 |}}

**7-** Select Human as species (by default).

**8-** In the //Function level analysis//, check both checkboxes, //Gene ontology// and //Uniprot keywords//.

**9-** In the //Pathways// panel select all the pathways (by default).

**10-** In the //Study information// panel, press the //File browser// button and select the desired output folder. In this case we will use //analysis_BRCA//. Give a name to the study, for example "BRCA Differential signaling".

{{ :hipathia_work3_5.png?600 |}}

**11-** Press the //Run analysis// button. A study will be created and listed in the studies panel. You can access this panel by clicking on the //My studies// button.