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of all pairwise weighted Robinson-Foulds distances using the Ward method [57]. Four main clusters are found, each one representing one of the four peptidome subsets. The proteome -based GBDP tree ...
proteins are a relevant source of TAP-C ligands Different features of the parental proteins from the four datasets were analyzed. The parental proteins for TAP+, TAP-NC, and HLA-II ligands had similar ...
frequencies at non-anchor positions in our HLA peptidomics data and in the human proteome (r = 0.85) (Fig 3 and Fig J in S1 Supporting Information). The most important difference that could strongly affect ...
for the Human Proteome Organization (HUPO) Plasma Proteome Project(34). Although there are thousands of different proteins in plasma, the abundances of individual proteins differ by many orders of magnitude ...
volunteers. Results: We detected 427 different mass signals in the urine of healthy donors. Within- and between -day imprecision in relative signal intensities ranged from 1% to 14% and from 4% to 16 ...
that pathogens differ in their peptidomes —the pool of short peptides derived from the pathogen’s proteome —so that different pathogens select for different MHC variants with distinct peptide-binding properties ...
Human plasma is a complex fluid that contains more than 3000 individual proteins and peptides in quantities ranging from nanograms to tens of grams per liter (1)(2). The plasma proteome and peptidome ...
< .001) in the second validation cohort. No survival difference could be observed between both classifications in the control set. Interestingly, parallel application of the 8-peptide algorithm to plasma ...
proteins between 25 and 250 amino acids in length. The translated ORFs were then sequentially queried for the presence of an amino-terminal cleavable signal peptide, the absence of transmembrane domains ...
to accurately assign AMP genes as orthologs. Clustered analysis of sequences (CLANS) analysis Sequence similarity between identified AMP candidate groups was visualised using the Clustered Analysis of Sequences ...
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