Additional Information


All code for DeCoaD written at the NCBI is released into Public Domain. The licenses of external components are indicated in the source packages.


DeCoaD should be cited as follows:

  • M. B. Hamaneh and Y.-K. Yu. Relating diseases by integrating gene associations and information flow through protein interaction network, PLOS ONE, 9(10): e110936. doi:10.1371/journal.pone.0110936.


  • Mehdi Bagheri Hamaneh and Yi-Kuo Yu designed the study, conducted the research and wrote the paper.

  • Mehdi Bagheri Hamaneh wrote most of the code for the web service.

  • DeCoaD heavily relies on qmbpmn-tools written by Aleksandar Stojmirovic.


DeCoaD web server is written in the Python programming language and relies on several open-source components:

The web browser client code uses various Javascript routines from the NCBI and elsewhere. ECMAScrpit code and widgets for the SVG ‘Network Navigator’ were taken from Carto:Net

All discrete network image color schemes were taken from the site by Cynthia A. Brewer, Geography, Pennsylvania State University.

The gene-disease association data and hierarchical disease relations are obtained from the Comparative Toxicogenomics Database (CTD).

The protein-protein interaction network is created using ppiTrim, a program that processes iRefindex, which incorporates entries from all major protein interaction databases.

SaddleSum term datasets are based on the Gene Ontology (associations downloaded from the NCBI FTP site) and the KEGG Pathways Database.

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