ConfeitoGUI

★ Example 1

♦ A dataset for example

• A dataset of Affymetrix grape microarray experiments (the dataset is here).
  Rows and columns represent probes and experiments, respectively.
• 439 experiments (a list of the experiment is here)
• 16,436 probes (a list of probes is here)

♦ Purpose of Example 1

• The collection of genes that are specifically expressed in grape skin.
• For that, the selection of experiments about grape skin.
• The making of a correlation matrix between experiments.

♦ Preparation

• Using the R platform, the dataset was transposed to calculate correlation between experiments (vvixgmat.txt).

♦ Methods

Making a correlation matrix Click launch.bat to open ConfeitoGUI. Click Correlation Tool in the Init Tool tab to open the Correlation Tool window. In the Input File section, click “Browse” and select “vvixgmat.txt”. In the Task section, select a type of correlation coefficient (select “Cosine”). In the Output Folder section, select an output folder (make and select “cor”). Push the Start button to execute the calculation.

Preprocessing for network analysis Click Preprocessing Tool to open the Preprocessing Tool window. In the Correlation Data Folder section, browse and select “cor”. In the Output File section, browse this folder and name “vvicor.flis”, and then push the select button. Push the Start button to make the file “vvicor.flis”. Push “x” at the topright corner of the Preprocessing Tool window to close the window. Click the Check Tool button to open the Check Tool window. In the Correlation Data File section, browse and select “vvicor.flis”. Click the Start button to execute.

Analysis Click the Confeito Analysis tab and select Analysis Menu (select “FPO” in this example). In the Correlation Data File section, browse and select “vvicor.flis”. In the Correlation Data Type section, select Cosine. In the Output Folder section, make and select an output folder (make and select “fpo”). Push the Start button to execute.

Results Open the output folder (“fpo”). Open the file “result.net” using a software for network analysis (such as Pajek). Draw a network using the file. Check experiments of interest (X285 to X292 for experiments of grape skin). In the network, these experiments were separated into two network modules. In this case, a larger network module is better for the purpose.

Re-analysis for obtaining a larger network module including experiments of interest Click the Confeito Analysis tab in the Confeito GUI window. Click the Setting button in the Correlation Data Type section to open the FPO window. Click Open Advance Setting to open a window for advance setting. Change “Min ELement” into 5 (the larger number, the larger network module to get). In the Output Folder section, make and select “fpo2” folder. Push the Start button. After the re-analysis, open “result.net” in the “fpo2” folder using Pajek and depict a network. In the network, experiments of interest belong to a single network module.

• To know the way of the FNI analysis, click here.

♦ Tips for re-analysis

• In the case to increase the size of a network module of interest, increase “Min Elements”, “Advance Setting”, “Setting”.
• In the case to decrease the size, decrease “Max Elements”.
• In the case to depict lines between elements in different widths according to a threshold of correlation coefficient, input the threshold (default value is 0.9)
  “Correlation Data Type” -> “Setting” -> “Open Advanced Setting” -> “Solid Bold (FPO)”.

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