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Alzheimer's disease (AD) is a chronic neurodegenerative disease with significant financial costs and negative impacts on quality of life. Psychotic symptoms, i.e., the presence of delusions and/or hallucinations, is a frequent complication of AD. About 50% of AD patients will develop psychotic symptoms (AD with Psychosis, or AD + P) and these patients will experience an even more rapid cognitive decline than AD patients without psychosis (AD-P). In a previous analysis on medication records of 776 AD patients, we had shown that use of Vitamin D was associated with delayed time to psychosis in AD patients and Vitamin D was used more by AD-P than AD + P patients. To explore the potential molecular mechanism behind our findings, we applied systems pharmacology approaches to investigate the crosstalk between AD and psychosis. Specifically, we built protein-protein interaction (PPI) networks with proteins encoded by AD- and psychosis-related genes and Vitamin D-perturbed genes. Using network analysis we identified several high-impact genes, including NOTCH4, COMT, CACNA1C and DRD3 which are related to calcium homeostasis. The new findings highlight the key role of calcium-related signaling pathways in AD + P development and may provide a new direction and facilitate hypothesis generation for future drug development.
Pubmed ID: 32273551 RIS Download
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Open-source software for network visualization and analysis helping data analysts to intuitively reveal patterns and trends, highlight outliers and tells stories with their data. It uses a 3D render engine to display large graphs in real-time and to speed up the exploration. Gephi combines built-in functionalities and flexible architecture to: explore, analyze, spatialize, filter, cluterize, manipulate and export all types of networks. Gephi runs on Windows, Linux and Mac OS X. Gephi is based on a visualize-and-manipulate paradigm which allow any user to discover networks and data properties. Moreover, it is designed to follow the chain of a case study, from data file to nice printable maps. It is open-source and free (GNU General Public License). Applications: * Exploratory Data Analysis: intuition-oriented analysis by networks manipulations in real time. * Link Analysis: revealing the underlying structures of associations between objects, in particular in scale-free networks. * Social Network Analysis: easy creation of social data connectors to map community organizations and small-world networks. * Biological Network analysis: representing patterns of biological data. * Poster creation: scientific work promotion with hi-quality printable maps. Gephi 0.7 architecture is modular and therefore allows developers to add and extend functionalities with ease. New features like Metrics, Layout, Filters, Data sources and more can be easily packaged in plugins and shared. The built-in Plugins Center automatically gets the list of plugins available from the Gephi Plugin portal and takes care of all software updates. Download, comment, and rate plugins provided by community members and third-party companies, or post your own contributions!
View all literature mentionsSystem that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in absence of direct experimental evidence. Orthologs view is curated orthology relationships between genes for human, mouse, rat, fish, worm, and fly.
View all literature mentionsDatabase of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations and are derived from four sources: Genomic Context, High-throughput experiments, (Conserved) Coexpression, and previous knowledge. STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable. The database currently covers 5''214''234 proteins from 1133 organisms. (2013)
View all literature mentionsTHIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. An integrated software suite for functional analysis of experimental data. The scope of data types includes microarray and SAGE gene expression, SNPs and CGH arrays, proteomics, metabolomics, pathway analysis, Y2H and other custom interactions. MetaCore is based on a proprietary manually curated database of human protein-protein, protein-DNA and protein compound interactions, metabolic and signaling pathways and the effects of bioactive molecules in gene expression.
View all literature mentionsIntegrated database resource consisting of 16 main databases, broadly categorized into systems information, genomic information, and chemical information. In particular, gene catalogs in completely sequenced genomes are linked to higher-level systemic functions of cell, organism, and ecosystem. Analysis tools are also available. KEGG may be used as reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies.
View all literature mentionsSoftware Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
View all literature mentionsThe SciCrunch Infrastructure was developed as a cooperative data platform to be used by diverse communities in making data more FAIR.
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