EMCmodule: Discovery of transcription regulatory modules using evolutionary Monte Carlo

 

 

Mayetri Gupta, and Jun S. Liu (2005).

De novo cis-regulatory module elicitation for eukaryotic genomes

Proc. Natl. Acad. Sc. USA: 102 (20) pp. 70797084.

 

 

Supporting information

 

Supporting Text
Supporting Table 5
Supporting Table 6

Supporting Figure 4

Fig. 4. Red lines represent count statistics and motif scores for Bicoid (bcd), Caudal (cad), Hunchback (hb), Knirps (kni), and Kruppel (kr) putative binding sites found in the upstream sequences of the 15 Drosophila developmental genes reported in Berman et al. [Berman, B., Nibu, Y., Pfeiffer, B., Tomancak, P., Celniker, S., Levine, M., Rubin, G. & Eisen, M. (2002) Proc. Natl. Acad. Sci. USA 99, 757762]. Histograms show the same statistics based on the putative binding sites found in the 100 shuffles of the original data set.

Supporting Figure 5

Fig. 5. (a) Sequence logos for six motifs found by EMCMODULE by using JASPAR matrices as input. (b) The corresponding site locations.

 

Software:

 

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