Because PID does not comprehensively collect pathway interactions, many well-known pathway cross-talk pairs are not curated into PID.
We collected pathways from BioCarta, GenMAPP, GeneGo, and Ingenuity.
In addition, some cellular network or signaling pathway databases have systematically collected pathways associated with specific diseases reported in the literature [ 28, 29].
Many well-established databases--e.g., KEGG, WikiPathways, and BioCyc--are dedicated to collecting pathway data for public access.
CPBD collects pathway data from multiple databases, which results in a large degree of pathway duplication and overlap, making pathway consolidation necessary [ 18].
On the other hand, KEGG MODULE, a database that collects pathway modules and other functional units, presents a promising tool for functional classification [ 16].
ConsensusPathDB collects pathway data from many databases but dose not appear to produce integrated pathways--even when the same pathway is present in different sources, they are still listed individually without merging.
A database resource for studying functions of a biological system, Kyoto Encyclopedia of Genes and Genomes (KEGG) collected pathway information on the molecular interaction and reaction networks, which helps conduct pathway-based analysis to study genes of unknown biological systems.
Initially, we build a protein network of pathways by collecting KEGG AD pathway and its neighbor pathways.
We collected 168 pathways from PID after removing redundant and less informative pathways (Additional file 2).
