Volume 10, Issue 4, Pages 652-655 (April 2017) TomatoNet: A Genome-wide Co-functional Network for Unveiling Complex Traits of Tomato, a Model Crop for Fleshy Fruits  Hyojin Kim, Bong Suk Kim, Jung Eun Shim, Sohyun Hwang, Sunmo Yang, Eiru Kim, Anjali S. Iyer-Pascuzzi, Insuk Lee  Molecular Plant  Volume 10, Issue 4, Pages 652-655 (April 2017) DOI: 10.1016/j.molp.2016.11.010 Copyright © 2017 The Author Terms and Conditions

Figure 1 TomatoNet Is Highly Predictive for Fruit Development and Other Pathways. (A) Major network communities in the largest component of the 500 000 most significant links of TomatoNet were identified using an overlapping module detection software, CFinder, and were indicated by different color codes. Significantly associated pathway terms for each community are listed along with their significance scores. (B) FR network, a network of fruit development and ripening genes by TomatoNet. Among 211 tomato FR genes derived from the FR database, 131 genes were connected by TomatoNet links. Tomato-specific genes that do not have orthologs in Arabidopsis or rice are represented as red nodes, and network links inferred by only tomato-specific genomics data are represented as red edges. (C) Significance of the connected 131 FR genes by TomatoNet was tested by distribution of the number of within-group edges among 1000 random samples of 131 tomato genes. The number of within-group edges of the FR network is significantly higher than random distribution (P < 0.001, Z-test). (D) Fold enrichment of fruit ripening genes and fruit development-ripening genes among top candidates by context-associated predictions of TomatoNet using 100 upregulated genes 10 days after breaker-stage fruit compared with the mature green stage and flower stage, respectively, as input data. Molecular Plant 2017 10, 652-655DOI: (10.1016/j.molp.2016.11.010) Copyright © 2017 The Author Terms and Conditions