EClerize: A customized force-directed graph drawing algorithm for biological graphs with EC attributes

Danaci H. F., Cetin-Atalay R., ATALAY M. V.

JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, cilt.16, sa.4, 2018 (SCI-Expanded) identifier identifier identifier

  • Yayın Türü: Makale / Tam Makale
  • Cilt numarası: 16 Sayı: 4
  • Basım Tarihi: 2018
  • Doi Numarası: 10.1142/s0219720018500075
  • Dergi Adı: JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY
  • Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus
  • Anahtar Kelimeler: Biological graph, enzyme, EC number, Cytoscape, network visualization, LAYOUT ALGORITHM, PATHWAYS, VISUALIZATION, ENVIRONMENT, CYTOSCAPE
  • Orta Doğu Teknik Üniversitesi Adresli: Evet

Özet

Visualizing large-scale data produced by the high throughput experiments as a biological graph leads to better understanding and analysis. This study describes a customized force-directed layout algorithm, EClerize, for biological graphs that represent pathways in which the nodes are associated with Enzyme Commission (EC) attributes. The nodes with the same EC class numbers are treated as members of the same cluster. Positions of nodes are then determined based on both the biological similarity and the connection structure. EClerize minimizes the intra-cluster distance, that is the distance between the nodes of the same EC cluster and maximizes the inter-cluster distance, that is the distance between two distinct EC clusters. EClerize is tested on a number of biological pathways and the improvement brought in is presented with respect to the original algorithm. EClerize is available as a plug-in to Cytoscape (http://apps.cytoscape.org/apps/eclerize).