Pan-Grass Syntenic Gene Set (sorghum referenced)
datasetposted on 13.03.2016 by James Schnable, Yang Zang, Daniel W. C. Ngu
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
Syntenic gene lists for sorghum, both maize subgenomes, setaria italica, setaria viridis, oropetium, rice, and brachypodium. Initial homology search conducted with lastz. Syntenic regions identified using QuotaAlign (https://github.com/tanghaibao/quota-alignment). One to one gene pair identification performed using the method describe in Zhang et al 2017.
Zhang Y, Ngu DW, Carvalho D, Liang Z, Qiu Y, Roston RL, Schnable JC. (2017) “Differentially regulated orthologs in sorghum and the subgenomes of maize.” The Plant Cell doi: 10.1105/tpc.17.00354 bioRxiv preprint doi: 10.1101/120303