ConfeitoGUI: A toolkit for size-sensitive community detection from a correlation network

PLoS One. 2018 Oct 23;13(10):e0206075. doi: 10.1371/journal.pone.0206075. eCollection 2018.

Abstract

Analysis of the large amounts of data accumulated in public databanks can facilitate a more comprehensive understanding of molecular biological processes. Community detection from molecular biological data is paramount in characterizing evolutionary and functional traits of organisms based on gene homology and co-expression, respectively. Although there are common tools to detect local communities from a large network, no toolkit exists for detecting communities that include an element of interest based on size sensitivity, i.e., functionality to obtain local communities with preferred sizes. Herein, we present the ConfeitoGUI toolkit for detecting local communities from a correlation network involving size sensitivity. We compared the toolkit with other common tools for detection in reconstructing communities of microarray experiments of mice. In the results, ConfeitoGUI was observed to be preferable for detecting communities whose sizes are similar to those of original communities compared to other common tools. By changing simple parameters representing sizes for the toolkit, a user can obtain local communities with preferred sizes, which is beneficial for further analysis of members belonging to the communities.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Animals
  • Computer Graphics*
  • Humans
  • Martial Arts
  • Mice
  • User-Computer Interface*

Associated data

  • Dryad/10.5061/dryad.jc247v3

Grants and funding

This work was supported, in part, by Grants-in-aid for Scientific Research (C) (no. 26350967; https://www.jsps.go.jp/english/e-grants/; external) and Scientific Research on Innovative Areas (no. 25108727; https://www.jsps.go.jp/english/e-grants/grants01.html; external) from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan, by the Kazusa DNA Research Institute Foundation (internal) (HS), and by the Promotion of Dissimilar Field Collaboration Research at Osaka Prefecture University (grant no. 0203041700; http://www.iao.osakafu-u.ac.jp/urahp/?page_id=28 [in Japanese]; internal) (YO). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. There was no additional external funding received for this study.