PMC:4331682 / 22025-23964 JSONTXT

{"project":"2_test","denotations":[{"id":"25707987-22912671-14887599","span":{"begin":134,"end":136},"obj":"22912671"},{"id":"25707987-21177658-14887600","span":{"begin":151,"end":153},"obj":"21177658"},{"id":"25707987-21177658-14887601","span":{"begin":1169,"end":1171},"obj":"21177658"},{"id":"25707987-18000002-14887602","span":{"begin":1245,"end":1247},"obj":"18000002"},{"id":"25707987-14681454-14887603","span":{"begin":1255,"end":1257},"obj":"14681454"},{"id":"25707987-18988627-14887604","span":{"begin":1266,"end":1268},"obj":"18988627"},{"id":"25707987-19897547-14887605","span":{"begin":1277,"end":1279},"obj":"19897547"},{"id":"25707987-19850723-14887606","span":{"begin":1294,"end":1296},"obj":"19850723"},{"id":"25707987-21177658-14887607","span":{"begin":1468,"end":1470},"obj":"21177658"}],"text":"To assess the performance of the proposed method, we tested the proposed network alignment method based on PPI networks in NAPAbench [25] and IsoBase [26]. NAPAbench is a network alignment benchmark that consists of 3 different datasets, referred to as the pairwise alignment dataset, 5-way alignment dataset, and 8-way alignment dataset. Each dataset contains three different subsets of 10 network families, each subset created using a different network growth model - CG (crystal growth), DMC (duplication-mutation-complementation), and DMR (duplication with random mutation). Each network family consists of 2, 5, or 8 PPI networks depending on the alignment dataset. For network families in the pairwise alignment dataset, each family contains one network with 3,000 nodes and the other with 4,000 nodes. In the 5-way network alignment dataset, a network family consists of 5 networks with 1,000, 1,500, 2,000, 2,500, and 2,500 nodes. Finally, in the 8-way alignment dataset, every network family consists of 8 networks, where each network contains 1,000 nodes. To evaluate the performance of the proposed method on real PPI networks, we utilized IsoBase datasets [26], which was constructed by integrating the following databases: BioGRID [27], DIP [28], HPRD [29], MINT [30], and IntAct [31]. IsoBase contains the PPI networks of five species: H. sapiens, M. musculus, D. melanogaster, C. elegans, and S. cerevisiae. Currently, the PPI network of H. sapiens in [26] has 22,369 proteins and 43,757 interactions, the PPI network of M. musculus has 24,855 proteins and 452 interactions, the PPI network of D. melanogaster has 14,098 proteins and 26,726 interactions, the PPI network of C. elegans has 19,756 proteins and 5,853 interactions, and the PPI network of S. cerevisiae has 6,659 proteins and 38,109 interactions. In our analysis, we excluded the M. musculus network as it currently contains only a small number of interactions."}