EMCmodule: Discovery of transcription regulatory
modules using evolutionary
Mayetri Gupta, and Jun S. Liu (2005).
De novo cis-regulatory module elicitation for eukaryotic genomes
Proc. Natl. Acad. Sc. USA: 102 (20) pp. 7079–7084.
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, 757–762]. 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.
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