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• W2297170634 abstract "Apoptosis is a type of cell death mediated by different signaling pathways involving protein-protein interactions that eventually activate caspases, a family of proteases capable of degrading cellular proteins. In this study we identify genes that belong to 16 protein families known to be involved in apoptosis in 5 vertebrate genomes: human, mouse, rat, Danio zebrafish, and Fugu pufferfish. It is shown that most apoptotic pathways are conserved in these vertebrate genomes, whereas key genes of the Fasmediated extrinsic pathway have not yet been identified in zebrafish and pufferfish genomes. Sequence alignment indicates that the upstream regions are less conserved than the corresponding transcript sequences and the sequence identity further declines after masking out the repetitive elements in the upstream sequences. These data are critical for phylogenetic footprinting studies of apoptosis genes in vertebrate genomes. Based on 366 known protein-protein interactions covering 168 (-72%) human apoptosis genes, we assemble a protein interaction network. To facilitate human visualization and potentially help biologists in apoptosis research, a two-layer protein interaction network is built for each human apoptosis gene. Several known apoptotic complexes, such as apoptosome, DISC, inflammasome and TNFRI complex, are all visualized in the two-layer interaction networks. We hypothesize that these two-layer protein interaction networks may help infer other multi-protein complexes in apoptosis. Furthermore, we computationally identify putative transcription factor (TF) binding sites upstream of apoptosis genes, and use protein-protein interactions in conjunction with phylogenetic footprinting information for prediction filtering. Our results suggest that protein-protein interaction data could complement sequence conservation to reduce" @default.
• W2297170634 created "2016-06-24" @default.
• W2297170634 creator A5082156610 @default.
• W2297170634 date "2004-01-01" @default.
• W2297170634 modified "2023-09-24" @default.
• W2297170634 title "Computational detection of transcriptional regulators of protein complexes in apoptosis" @default.
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• W2297170634 hasPublicationYear "2004" @default.
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