If the ith gene produces a product x that matches a binding site in the jth gene, then the ith gene may regulate the expression of the jth gene.
Surprisingly, the de novo motif-binding program also identified a second common consensus (hereafter termed "de novo"; Figure 1C, e value = 6.5e−95) that appears to be a hybrid site: its 3′ portion matches a binding motif previously identified for the homeodomain protein MEIS1 (MEIS1_2335.1, uniprobe, UP00186, p = 0.000185), while the 5′ is similar to the selex NKX2-5 -bindingg NKX2-5 -binding
Interestingly, out of 206 de novo motifs, 126 appear to match a known transcription binding motif and, of these, 75% have been shown to play a role in gene regulation in a particular tissue.
Rule 2: REL - of - P i - PREP - P j This rule is intended to match a phrase like "binding of P0 to P1" as shown in the example in Figure 1-R2.
When scanned against the TRANSFAC database [57], this conserved region perfectly matches a 6 bp binding site for the Achaete-Scute family of transcription factors.
For perspective, the 4th most abundant tag with a normalized count of 4,903 tags matches a chlorophyll a/b binding factor as do several of the most abundant tags (Additional file 2).
Here, we have identified an Mrg-binding motif within Cap-H2 that matches a predicted Mrg15 protein-binding consensus sequence (FxLP) derived from structure function studies of the MRG domain as well as sequence analysis of Mrg15 interactors (Xie et al. 2012).
The 5' element (5' GTAAACA-3' GTAAACA-3ignated A1) matcherea computationally-idesignatedFOXP3 binding element obtA1ned via ChIP-chip experimatchedG/a T/c AAACA, Figure 2A) [30].
Scatchard analysis of I-27.F7 binding to SK-BR-3 cells revealed a two-mode pattern of binding, which matches a model with binders of two different avidities (see Figure 3) [ 31].
