Systems Analysis of Arrestin Pathway Functions - Progress in Molecular Biology and Translational Science - page 428

familywise error rate. 99 A Bonferroni approach can also be applied to reduce
error rate. This technique multiplies the uncorrected p -value by the number
of genes tested, treating each gene as an individual test. This method
increases significant data specificity by reducing the number of false positives
identified. However, this benefit is at the cost of reduced array sensitivity as
the number of potential false negatives increases. A modification of the
Bonferroni approach, the false discovery rate (FDR), uses a random permu-
tation while assuming each gene is an independent test. In addition, boo-
tstrapping approaches can improve significantly on the Bonferroni
approach, as they are less stringent. 100 Resampling-based FDR-controlling
procedures can also be used. 101 These data extraction protocols can be
generically applied easily to other mass analytical array platforms, for exam-
ple, antibody/protein arrays. 102 However, one caveat is of course required
in cases of protein/antibody arrays, that is, the likelihood of high logarithmic
increases in protein expression is unlikely as even modest changes of protein
expression 103 may be sufficient to generate profound signaling actions, espe-
cially if the protein possesses enzymatic or scaffolding activity, such as
b -arrestin. As stated, many of these analytical techniques can be easily trans-
ferred between genomic and proteomic platforms; however, while most
transcriptomic platforms are standardized, MS detection of proteins from
a complex sample is actually a random discovery process. The eventual bio-
informatic annotation of these massive datasets provides an invaluable
approach for elucidation of the physiological interpretation of the data.
The application of statistical informatic annotation is especially important
for MS proteomics as this provides a vital support, via functional protein
clustering, for the unavoidable variability of protein detection between
experiments. This important aspect of functional annotation of proteomic
data will be expanded upon in subsequent sections.
3.2. Global proteomic analysis
Global proteomic analysis of molecular signaling systems or disease processes
is rapidly becoming a standardized laboratory technique for the investigation
of complex biological systems. 61,19,104,105 As GPCR-based b -arrestin signal-
ing pathways have been demonstrated to control both genomic transcription
and eventual protein translation, 26,56-59 a combined approach to integrate
both proteomic and transcriptomic analysis of b -arrestin signaling paradigms
seems prudent. However, there are several considerations that are required
when employing such an integrated analytical approach. The primary