# Dec 20, 2010

YY1 motif:

1. GCCATnTTG (YY1 motif reported in Xie X. et al (Kellis lab), Nature, 2005

2. YY1 motif model from JASPAR (Homo sapiens; ID: MA0095.1)

        C  C  A  T
A  [ 6  0  0 17  0  3 ]
C  [ 1 16 17  0  0  8 ]
G  [ 7  0  0  0  0  3 ]
T  [ 3  1  0  0 17  3 ]

Searched for motifs in all four YY1 clusters using online tool: http://motif.bmi.ohio-state.edu/ChIPMotifs

Used UCSC track browser to generate FASTA sequences from GFF; used scripts/makeGFFcompatibleWithUCSC.py to make UCSC compatible

Only cluster 2 contained the canonical YY1 motif (above). Cluster 4 showed a CCAT, but preceeded by Ts (not reported as YY1 by STAMP)