The model was verified experimentally, and compiled test results were used for this purpose.
This data set is mainly derived from one-at-a-time experimentally demonstrated interactions compiled through a literature curation process [ 13], which suggests a high degree of reliability.
All available protein sequences for T. gondii and C. parvum that emerged from various gene prediction approaches or were experimentally derived are compiled into a hypothetical proteomes for each of the respective organisms in order to be able to search the proteomics data with the most comprehensive and unbiased dataset possible.
The optimization of the rate constants was started from a set of rates compiled from experimentally determined reaction rates and estimates from the steady state reconstruction [13].
For the markers selected by the previous steps, we examined which ones had a Gene Ontology annotation as being extracellular, or were part of the experimentally derived Human Plasma Proteome list compiled by Anderson et al. [23].
F-match searches against the largest library (>500) of position specific scoring matrices (PSSM) compiled on experimentally verified transcription factors binding sites of the higher eukaryotes [20], [21] from the TRANSFAC database [20].
Scanning 302 HIV-1 proteomes, corresponding to 2,718 HIV-1 protein sequences, resulted in the identification of 22,779 epitope motifs, including 8,208 experimentally defined CTL epitopes compiled in databases prior to our study (the latter two figures include redundancies from detection of the same epitopes in multiple individuals).
Similar to our previous study, 10 the protein sequence data used in this paper come from O-GlycBase 11 (Version 6.00), which contains experimentally verified glycosylation sites compiled from protein databases.
To further verify that the processes found regulated were consistent with real data and not just target predictions, we tested for enrichment among the experimentally validated targets (as compiled in the miRTarBase database [ 27]) for the regulated miRNAs among the robust dataset of differentially expressed mRNA that we had described in prior work [ 16].
The development of multiple methods that compile experimentally derived protein interactions from curated databases, process the interaction graphs, cluster related modules, discover novel associations and visualize them [ 77, 78] appears to have out-shined valuable genome-aware inference methods.
