HPRD (Peri et al., 2004) contains manually curated proteomic information regarding human proteins, which are annotated and linked to OMIM database (Hamosh et al., 2005). Primary sources of PPI data include BioGRID (Stark et al., 2006), DIP (Xenarios et al., 2000), HPRD (Peri et al., 2004), IntAct teorchard2013mintact, and MINT (Licata et al., 2012).ĭIP (Xenarios et al., 2000) was the first database, which combined information from multiple observations and experimental techniques into networks of interacting proteins for different species. Nowadays, PPIs of species and associated data are stored in many databases, which usually are weekly or monthly updated. The collection of PPI data yields a network depicting a global overview of the relationships between proteins. They represent all known physical interactions between proteins within a cell. In the last 10 years, there has been a rapid growth of available protein–protein interaction (PPI) data. We also provide tools for visualizing and comparing such networks, in order to identify the expression and interaction changes of proteins across tissues, or between the normal and pathological states of the same tissue. SPECTRA integrates gene expression and protein interaction data from the most authoritative online repositories. In this paper, we present SPECTRA, a knowledge base to build and compare tissue or tumor-specific PPI networks. For these reasons, a great attention has been recently paid to tissue-specific PPI networks, in which nodes are proteins of the global PPI network whose corresponding genes are preferentially expressed in specific tissues. Indeed, proteins can form tissue-selective complexes, while they remain inactive in other tissues. They ignore the specific set of tissues or tumors where the interactions take place. Protein–protein interaction (PPI) networks available in public repositories usually represent relationships between proteins within the cell.
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