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Chromatin modification clusters are ranked in decreasing order of retention or increasing order of splice site usage in H using a Wilcoxon test with a p-value cutoff of 10−5.
Certain chromatin modification clusters in H appear to be analogous to ones in IMR90 based on the patterns of modifications, such as the "enhancer-like" state 1 (H) with state 1 (IMR90), and the "promoter-like" state 5 and state 6 (H) with state 2 (IMR90).
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SfIV phage orfs 25 27 encode for the O-antigen modification cluster.
Akin to the NHLP system, previous informatics work has shown that the Bacillus anthracis and B. cereus TOMM precursors are encoded more than one megabase away from the modification cluster [ 30].
Since the type I restriction modification cluster is clearly transcriptionally activated in the outbreak strains, it will be interesting to follow up if their expression has provided them with a resistance and virulence advantage compared to J2315 as an ancestral ET12 isolate.
Recently, we showed a mix-and-match relationship between families of precursors and families of maturation enzyme; the nitrile hydratase-related leader peptide (NHLP) and Nif11-related leader peptide (Nif11LP) can associate with a single type of export transporter but with multiple types of modification cluster [ 6].
As expected, DNA segments with none of the ten features (cluster 25) or with only negative histone modifications (clusters 23 and 24) were rarely active in the enhancer assay.
This is most clearly seen in the ribosomal large subunit, where modifications cluster in highly conserved areas of the ribosome devoted to peptidyl transfer, sites of A- and P tRNA binding, the peptide exit tunnel and intersubunit bridges [1] [4].
Their best characterized targets are small nuclear RNAs (snRNAs) and ribosomal RNAs, where many of these post-transcriptional modifications cluster in functionally important regions and contribute to efficient ribosome biogenesis and/or function.
Seventeen genes were associated with phosphorylation (cluster 4 in Figure 4) or protein modification process (cluster 5 in Figure 4).
The initial parameter settings for the modification mass cluster centers, shared for all three algorithms, were initialized randomly within the range of modification masses in the input dataset.
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