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The model of macrophage signalling and effector pathways presented here is to our knowledge the most comprehensive pathway of its kind published to date.
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Because the IntPath database is currently the most powerful tool and also the most comprehensive integrated pathway database, we first conducted pathway analysis using the IntPath database [ 50] to draw the genetic networks related to EGFR and ANXA3.
For pathway enrichment analysis, we use the IntPath database [ 24], which is currently one of the most comprehensive integrated pathway databases.
IntPath is currently one of the most comprehensive integrated pathway databases.
This tool can also be used to perform pathway-based data analysis by using high quality human-curated pathways in the Reactome database, the most comprehensive open source pathway database.
Comparison with GSA indicates that our method is comprehensive and efficient in terms of extracting weak signals and identifying pathways that are statistically significant but that a combination of GSA with GIENA provides the most comprehensive survey of pathway level dysregulation.
ConsensusPathDB in particular is one of the most comprehensive collections of pathways as it integrates more than 4,000 pathways from twelve data sources (see Table 1).
One of the most comprehensive sources of metabolic pathway data is the Roche Applied Science Biochemical Pathways chart (Michal, 1999).
Our tool is built upon the Reactome database, arguably the most comprehensive human curated open source pathway database, and leverages the highly reliable functional interaction network extracted from human curated pathways.
To construct the human cellular signaling network, we manually curated signaling pathways from the BioCarta database, which so far is the most comprehensive database for cellular signaling pathways.
The PPS is the most comprehensive software to simulate degradation pathways.
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