At last, differentially accumulated protein spots were determined according to statistically significant changes between samples by Student's t-test (abundance variation at least 2-fold, p < 0.05).
To test significant abundance of IUPs among hub proteins Student's t-test was performed and p values were calculated with the aid of "GraphPad QuickCalcs" (http://www.graphpad.com/quickcalcs/ttest1.cfm?Format=SD).
A semiparametric generalized additive logistic model (GAM) was used to test whether abundance of each motif differed between genes in the FG and BG sets [ 77, 79].
Wilcoxon test for abundance of NF-κB binding sites in NF-κB related genes in comparison to shuffled and random sequences.
Wilcoxon test of abundance [ 33] (Table 4) shows that there is a statistically significant difference between the randomly generated and shuffled real promoter sequences and the promoter sequences of NF-κB-dependent genes in dataset.
Four sites with varying cultural uses were surveyed monthly for eight months along a creek in Texas, and analysis of the data included chi-square and Kruskal Wallis tests, and abundance indices comparing material types across sites.
While these motifs need to be further characterized and experimentally tested, the abundance of known and putative phosphorylation sites is not surprising as eukaryotic genomes contain hundreds of kinases that exert a profound influence on cellular activity.
Data compilation, Mann–Whitney tests, Jaccard abundance index, Sørensen similarity index, and Spearman correlation were carried out using Microsoft Excel and SPSS (Version 16.0) (SPSS Inc. 2007).
t-tests on abundance per surface area of GC samples revealed similar results as calculations per sample area, with similarly low abundances found in the seep habitat types (mussel and tubeworm: p=0.150; seep and non-seep both: p=0.003).
In addition, to verify the findings from the pilot phase we have tested the abundance of a panel of four candidate serum proteins (α-2-HS-glycoprotein, apolipoprotein AI, clusterin and vitronectin) by immunoassays.
