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Another 33.8% of signatures were constantly expressed, defined by Meyers et al. (2004) [ 24] as those signatures with a summed abundance within a two-fold range (expression ratio <2).
The distributions of cleavage sites of ions observed in the MS/MS spectra were analyzed by summing the abundances of all fragment ions associated with a specific cleavage site and dividing by the summed abundance of all fragment ions in a given MS/MS spectrum.
In most MS approaches, the substrate protein is digested into peptides and the degree of phosphorylation at one site is calculated based on the summed abundance of the peptides containing this site.
Support for community assembly rules would require negative relationships between the observed abundance of each species and the summed abundance of all other ant species.
Population abundances of most ant species were correlated with both randomized expectations and the summed abundance of all other ant species.
Similar(55)
It is advised that researchers performing future proteome-wide quantitative studies compare their summed abundances to the estimates given here as a crude sanity check.
After accounting for both species (Wald X2 = 15,172, df = 16, P < 0.001) and island (Wald X2 = 9,516, df = 10, P < 0.001), abundances increased with expected abundance values (Wald X2 = 22,177, df = 1, P < 0.001) (Fig. 3C) and decreased with the summed abundances of all other co-occurring species (Wald X2 = 96, df = 1, P < 0.001) (Fig. 3D).
Analysis of ant abundances among islands showed that after accounting for species (Wald X2 = 11,925, df = 16, P < 0.001), abundances increased with expected values (Wald X2 = 52,802, df = 1, P < 0.001) (Fig. 3A) and decreased with the summed abundances of all other co-occurring species (Wald X2 = 342, df = 1, P < 0.001) (Fig. 3B).
To obtain the expression level for each gene, we summed the abundance of signatures that match the sense-strand of the gene and are found only once in the Arabidopsis genome and transcriptome.
This technique is useful to evaluate the sum abundance of AKRs, nevertheless, it is useless for globally evaluating and comparing abundance of individual AKRs.
Total abundance (sum of normalized values) of ARISA fragments was 251, 360, 351 and 387 for the Phases I IV respectively.
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