Resources

Software

1. AtGGM2014, a program to query and utilize the Arabidopsis gene network AtGGM2014. (Download)

Described in the following paper:

  • Ma S, Bohnert HJ, Dinesh-Kumar SP. 2015. AtGGM2014, an Arabidopsis gene co-expression network for functional studies. Science China Life sciences 58: 276-286. [Full Text]

2. MotifIndexer, a program for de novo promoter motifs finding. (Download)

Described in the following paper:

  • Ma S, Bachan S, Porto M, Bohnert HJ, Snyder M, Dinesh-Kumar SP. 2012. Discovery of stress responsive DNA regulatory motifs in Arabidopsis. PLoS One 7: e43198. [Full Text]

3. MotifNetwork, to analyze promoter motifs over an Arabidopsis gene network. (Download)

Described in the following paper:

  • Ma S, Shah S, Bohnert HJ, Snyder M, Dinesh-Kumar SP. 2013. Incorporating Motif Analysis into Gene Co-expression Networks Reveals Novel Modular Expression Pattern and New Signaling Pathways. Plos Genetics 9: e1003840. [Full Text]

Note: These three pieces of software were developed during the PI’s postdoctoral work in the Dinesh-Kumar lab at UC Davis.

Datasets

Coming soon.