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Software


​MotifIndexer,  a de novo promoter motifs finding program. (Click here to download)

Described in the following paper:
  • Ma S, Bachan S, Porto M, Bohnert HJ, Snyder M and Dinesh-Kumar SP. (2012) Discovery of stress responsive DNA regulatory motifs in Arabidopsis. PLoS ONE 7:e43198. [Abstract] [Full Text]


MotifNetwork, a program to analyze promoter motifs over Arabidopsis gene co-expression network. (Click here to download)

Described in the following paper:
  • Ma S, Shah S, Bohnert HJ, Snyder M and Dinesh-Kumar SP. (2013) Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways. PLoS Genetics 9(10):e1003840 [Full Text]


AtGGM2014, a program to visualize the gene expression patterns of the gene modules identified from an Arabidopsis gene co-expression network. The network, also termed AtGGM2014, contains 662 gene co-expression modules that function in diverse plant signaling pathways. The program generates heatmaps showing these modules' expression patterns in different tissues or their regulation upon various stresses or hormones treatments. The program can also extract and plot gene sub-networks for the a specific module(s). (Click here to learn more) (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(3): 276-28 [Full Text]