To identify transcription factors that may be involved in this global reorganization of chromatin, we next explored the distribution of consensus binding motifs for differentially expressed HSPC-TFs across the most variable H3K9ac peak-regions (see Material and Methods).
We have created sequence logos for observing amino acid distribution of consensus positive sites, non-consensus positive sites, consensus negative sites, and non-consensus negative sites.
The bidirectional sequencing strategy and the average length of quality reads (Table 1) also impacted upon the length distribution of consensus sequences.
The distribution of consensus base ratio in extra-pulmonary isolates and that in simulated data are plotted together (See Figure 5).
For each blood stage and each metabolic pathway the fraction of consensus reactions per total number of pathway reactions was computed to uncover the distribution of consensus reactions among pathways (see Additional file 17).
We checked the frequency distribution of consensus modules to ensure that no biases were introduced by specific combinations of experiments and more specifically by the Park et al. dataset which generated the majority of the combinations.
Analyzing the probabilities P cc and P nn we can show that this is possible only for δ (N - 1) - α (M - 1) + β M - γ N < 0. Then the frequency of the consensus state (stationary distribution of consensus) is estimated from above as π c = β β M + γ N < β 2 β M + δ (N − 1 ) − α (M − 1 ).
In an alignment of mosquito RPS6 tails with the Anopheles H1 histones (Fig. 5), we note that while some degree of identity covers the entire histone H1 protein, the C-terminal half of the H1 histone has a higher proportion of identities to the RPS6 tail, as indicated by the distribution of consensus residues.
Given that mice have been used extensively as genetic models to study nuclear receptor signaling (e.g. [ 19]), we compared the frequency and distribution of consensus direct repeat response elements [RGKTCAniRGKTCA, i = 1 to 5] both in the mouse and human genomes (Table 1).
We next analyzed the distribution of PUF consensus motifs.
In figure 6, we show the distribution of the consensus sequences named after an Ensembl or UniGene reference species gene.
