PT  - JOURNAL ARTICLE
AU  - Tak Lee
AU  - Sohyun Hwang
AU  - Chan Yeong Kim
AU  - Hongseok Shim
AU  - Hyojin Kim
AU  - Pamela C. Ronald
AU  - Edward M. Marcotte
AU  - Insuk Lee
TI  - WheatNet: A genome-scale functional network for hexaploid bread wheat, <em>Triticum aestivum</em>
AID  - 10.1101/105098
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 105098
4099  - http://biorxiv.org/content/early/2017/02/06/105098.short
4100  - http://biorxiv.org/content/early/2017/02/06/105098.full
AB  - Gene networks provide a system-level overview of genetic organizations and enable the dissection of functional modules underlying complex traits. Here we report the generation of WheatNet, the first genome-scale functional network for T. aestivum and a companion web server (www.inetbio.org/wheatnet). WheatNet was constructed by integrating 20 distinct genomics datasets, including 156,000 wheat-specific co-expression links mined from 1,929 microarray data. A unique feature of WheatNet is that each network node represents either a single gene or a group of genes. We computationally partitioned gene groups mimicking homeologous genes by clustering 99,386 wheat genes, resulting in 20,248 gene groups comprising 63,401 genes and 35,985 individual genes. Thus, WheatNet was constructed using 56,233 nodes, and the final integrated network has 20,230 nodes and 567,000 edges. The edge information of the integrated WheatNet and all 20 component networks are available for download.