hiPathia

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
====== Circuit values ======

Here you will find descriptive information about the matrix of circuit values.

  * **Circuit values**: You can download the matrix of circuit values by clicking on //Circuit values//.
  * **Heatmap**: A heatmap is a graphical representation of the values of a matrix. A not-supervised clustering is performed on the data per columns (samples). A good separation between the two colors of the upper bar of the heatmap indicates that the differences between the two groups are big enough to discriminate between them.
  * **PCA**: A Principal Components Analysis is performed in order to see if the matrix contains information enough to separate between the two groups. 
  * **Circuit significance**: Ordered table of circuit significance. More significant circuits are displayed in the upper part of the table. For each circuit, the following information is shown:
    * **circuit/term**: Code identifying the circuit consisting in the name of the pathway to which it belongs and the effector (last) node of the Circuit (//pathway Name : Effector//).
    * **UP/DOWN**: Up when the circuit is up-regulated in the disease case, DOWN otherwise.
    * **statistic**: Statistic of the Wilcoxon test performed between conditions.
    * **p.value**: P-value of the statistic test.
    * **FDRp.value**: Adjusted p-value of the statistic test using the FDR method.
    * **Fold Change**: is a measure describing how much the ** circuit activity** changes between conditions.[[https://en.wikipedia.org/wiki/Fold_change|reed more about Fold Change]]
    * **logFC**: The logarithm to base 2 of calculated Fold change.