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We emphasize how SRM can generate molecular maps of protein complexes and extract quantitative information on the number, size, distribution, and spatial organization of macromolecules.
Shown are 2D gel maps of protein sulfenation in brain mitochondria isolated from 5- to 30-month-old rats (40 μg protein/gel).
Although such webs of intracellular interactions are increasingly well characterized, little is known about large-scale maps of protein interactions between cells.
The gplots package from Bioconductor was used to generate heat maps of protein sets [ 16].
We utilized peptide arrays, which provide semiquantitative maps of protein interaction regions (Katz et al., 2011; Shanks et al., 2014).
Large-scale maps of protein interaction networks have been constructed recently using high-throughput approaches to identify protein interactions [ 151- 155].
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Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association.
Our method follows a probabilistic approach applied to the results of fitting protein domains into maps of proteins and the computation of local cross-correlation coefficient measures.
As initial maps of protein-protein interaction networks, gene expression profiles, and other large-scale dataset types have become available for several model organisms [1] [15], machine-learning algorithms including Bayesian network, Markov random field, decision tree, and Support Vector Machine (SVM) approaches have been applied to these datasets to predict gene function [16] [25].
With the advent of genome-scale maps of protein-protein interactions and transcription factor-DNA binding data, available from different groups and through databases, such as TRANSPATH (http://www.biobase.de), BioCarta (www.biocarta.com), and STKE (www.stke.org), discrete dynamic models can capitalize upon these resources to derive the network architecture.
We also compared gene maps of protein-coding and rRNA genes encoded by the pigeonpea mitochondrial genome (ICPA 2039) with those of the other 11 sequenced plant species.
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