a tool for correlation network analysis

About ConfeitoGUI

♦ Abstract

ConfeitoGUI is a stand-alone tool for extracting local communities (or network module in this site), based on the Confeito algorithm. The Confeito algorithm is an algorithm to extract network modules from a correlation network.

♦ Usage

♦ Steps for analysis

  1. Array Data Converter (optional): to change raw data of microarray experiments by Affymetrix and Agilent into a text-formatted file.
  2. Correlation Tool: to create a correlation matrix between elements. Cosine and Pearson correlation coefficients are selectable.
  3. Preprocessing Tool: to make a two-column list composed of identifiers of elements and names of files including correlation data by elements.
  4. Check Tool: to check files of correlation data.
  5. FPO (False-Positive-Out) analysis: to select out elements that are highly and excusively correlated to each other and thus, are composed of a network module.
    • Among elements with high correlation coefficients to an element, there can be some elements with high correlation to any (or a lot of) elements; namely “false-positive” elements.
    • ConfeitoGUI can efficiently remove out such false-positive elements from a network module.
  6. FNI (False-Negative-In) analysis (optional): for a network module, to select out elements that are specifically related to the module, in spite of low correlation coefficient to the eleements included in the module, namely “false-negative” elements.
    • Using tools for detecting local communities from a network including the FPO analysis, it is difficult to detect such elements, because of low correlation coefficients to elements of the module.
    • By combining the FPO and FNI analyses, ConfeitoGUI can remove out false-positive elements and select out false-negative elements.

♦ Comparison with the other tools for community detection

To check the accuracy of network modules that are extracted from ConfeitoGUI, we obtained a dataset of mouse microarray experiments from Gene Expression Omnibus (GEO), NCBI and compared ConfeitoGUI with the other tools for community detection in their memberships of network modules.

♦ References

♦ The advanced version of ConfeitoGUI

The version in this site is an academic-free version. About the advanced (or full) version of ConfeitoGUI, ask Kazusa DNA Research Institute.

Back to the portal.

The KAGIANA Project (since 2006)

Copyright (C) 2015 All rights reserved Osaka Prefecture University & Kazusa DNA Research Institute