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For this purpose, we have extracted rules from disparate information sources to increase coverage: pathway database, ordinary differential equation (ODE) model and Petri-net.
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Figure 4 shows the average coverage per pathway, where at least one gene is present, for 540 pathway maps represented in GeneGo's MetaCore[ 24] database for genes available on KRM2 and KRM1 arrays.
We define accuracy and sensitivity relationships between read length, coverage and pathway recovery and evaluate the impact of taxonomic pruning on ePGDB construction and interpretation.
The MD microarray, described here as a targeted genomic approach, was populated with 384 maize genes largely comprising four important metabolic pathways with rigorous gene coverage within each pathway.
The coverages of pathways can be expanded with the incorporation of more biological processes, predicting involvement of protein members in pathways.
bThe coverage for each pathway is referred to as the fraction of candidate target-genes among all the pathway member genes.
We thank Sina Rostam for analysis of pathway coverage in KEGG maps.
Two fosmids calculated to provide greatest coverage of the pathway were selected for shotgun sequencing.
Our results indicate that the iterative probabilistic Psi-square algorithm gives better pathway coverage than hierarchical clustering of the same dataset, i.e., 66% compared to 50% (p-value <0.01 using Welch two-sample t-test).
Functional and pathway coverage of interactions.
More discussion of the pathway coverage can also be found in Additional file 1.
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