Peptides clustering analysis

The synovial arrays were incubated with the sera from patients with early and severe RA as well as healthy patients. Hierarchical clustering analysis revealed that autoreactive B-cell responses for citrullinated epitopes were present in a subset of patients with early RA, features which are predictive of the development of severe RA. In contrast, autoantibodies directed against native epitopes including several human cartilage gp39 peptides and type II collagen, were associated with features predictive of less severe RA. 

Fig. 64. Proteomic analysis with a SELDI-TOF-MS. In single marker analysis left), the relative intensity of the 3.5 KDa peptide was high in the ALPE group. In the hierarchical clustering analysis with marker candidates, the heat map in the ALPE group differed from those in the myoglobinuric acute renal failure and normal groups (p. 69)...

The analysis was first performed on the trial III Type I defect simulation since Fig. 5a shows similar free energy profiles for the three trials, we deemed analysis of a single trial to be sufficient. Skipping every second frame to reduce computation time, surface-bound structures (defined as peptide/surface distances below 1.2 nm) were clustered with an RMSD cutoff value of 0.2 nm. As noted above, we used only the second half of the trajectory for the clustering analysis to eliminate the transient part of the MetaD bias potential. Among 39,696 stmctures, 78 clusters... 

Fig. 6 Top three surface-bound cluster center confomiations from a clustering analysis of the Type 1, trial III defect simulation compared to the control simulation with no chain defects. Secondary structure is indicated by peptide backbone color. Purple designates an ot-helix, magenta a turn, and cyan a random coil. Silver and pink represent healthy and defective chains, respectively...

Figure 10.5 Cluster analysis, (a) A combination of unsupervised clustering and heatmap visualization. The Euclidean distance measure and Ward linkage are used. Peptide intensities are log-transformed and normalized to zero mean unit variance (row by row). The profiles of 27 non-small-cell lung cancer patients are intermingled with those of 13 healthy controls (columns) (b) Supervised analysis using 11 peptides with Benjamini-Hochberg adjusted p-values <0.001 results in two distinctive branches at the root of the tree. Two cancer profiles are grouped with those of the healthy controls. All but one of the peptides are upregulated in cancer samples.

The governing parameters for the long-range conversion of (5)-acyl isopeptides (41 X = [CHRCOl OH) to native peptide analogues (42 X = [CHRCO]j OH) via intramolecular S-to-N acyl transfer (Scheme 13) are shown by computational and statistical methods (principal component analysis and cluster analysis) of model... 

Miao, V., Coeffet-Le Gal M.-F. et al. (2005) Daptomycin biosynthesis in Streptomyces roseosporus cloning and analysis of the gene cluster and revision of peptide stereochemistry. Microbiology (Reading, England), 151,1507. 

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