Pathway Analysis & Data Mining for Gene Expression

Available on MAC or PC!    MS Internet Explorer,  FireFox and  Safari compatible.

MetaCore™ is 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. The analytical package includes easy to use, intuitive tools for data visualization, mapping and exchange, multiple networking algorithms and filters. MetaCore™ is available in two business models:

• Web portal access — Named or concurrent licenses that provide access to the company’s secure server using the Internet protected by Verisign.
• Enterprise solution — Installation of MetaCore™ behind the customer’s firewall. MetaCore™ becomes part of the intranet network and can be used as an internal informatics system. In house installations give customers hierarchical access to accounts, group sharing, and behind-the-firewall data exchange security.

Annual or multi-year licenses are available.

Product highlights - Data Mining & Pathway Analysis

• Analyze ANY experimental high-throughput data in the context of pathways, networks and maps - ideal for data mining and pathway analysis applications
• Identify affected pathways and networks for your lists of genes, proteins, transcripts or compounds
• Easy-to-use workflow wizards for data upload, analysis and interpretation for pathway analysis, gene expression and more
• Concurrently visualize and cross-validate different types of data from gene expression to pathway analysis
• Choose from ten network-creating algorithms and multiple filters for optimal data mining
• Take advantage of the annotated content database that took over 100 man-years to assemble
• Over 500 interactive maps with consensus knowledge of human biology
• Visualize mouse, rat, worm, fly, yeast and dog data on maps and networks
• Mine your data in real time: multiple data points, conditions, time-series, treatments through animated videos
• Apply disease, tissue, functional processes and sub-cellular localization filters to focus networks on information relevant to study
• Have total control over settings: your choice of ranges, colors, data sets, etc.
• Select, save & export high resolution images of pathways and networks for pathway analysis mapping

Data analysis tools

• Multiple ways to generate networks
  • 10 network-generating algorithms
  • Specificity filters for tissues, functional processes, sub-cellular localization, interaction mechanisms, species etc.
• Enrichment analysis in multiple ontology’s: GeneGo annotated processes, canonical pathways, GO processes and human diseases
• Statistical tests and scoring for network relevance to the dataset, functional processes, cellular pathways and transcription factors
• Multiple types of P-value calculations for enrichment analysis and network prioritization
• Multiple logical operations on networks and gene lists
• Over 2 million resolved synonyms for genes, proteins and compounds
• Custom network editing for all functions - gene expression, pathway analysis, etc.
• Query for genes, proteins, compounds, reactions, pathways, drugs and diseases

Curated content

• Unique manually curated database of human protein-protein, protein-DNA, Protein-RNA and protein-compounds interactions such as gene expression
• Human endogenous metabolism: enzyme-encoding genes, reactions and metabolites
• Three domains of human interactions: target-ligand, signaling and signal transduction and core metabolism
• Over 500 original canonical pathway analysis maps for signaling and metabolism
• Proprietary GeneGo ontology for cellular and molecular processes and human diseases
• Pre-built process and disease networks

Integration, visualization and management of experimental data from pathway analysis to gene expression and beyond

• Universal parser for molecular data: Affymetrix, Agilent, Illumina, GE Healthcare expression arrays, SNP arrays, siRNA and proteomics
• Unique parsers for metabolomics data and custom protein-protein interactions
• Interconnectivity and cross-referencing with P-values between maps, networks and functional processes
• Drug targets and associated drugs
• Disease genetic data and disease networks
• Seamless integration and file exchange with ResolverTM , GeneSpringTM , Spotfire’s Decision Site TM, ArrayTrack, GeneData’s Expressionist and Phylosopher products, Inforsense’s KDE, SciTegic’s Pipeline Pilot, Xenobase and other data analysis packages including our customers internal software and databases
• Instant mapping of multiple, heterogeneous experimental data sets onto functional maps and pathways
• Concurrent visualization of multiple data types on the same maps or networks
• Concurrent visualization of multiple experiments, time points & dosages through animated graphics
• Flexible switching between data sets and controls
• User controls: colors scheme, value ranges, thresholds
• Mapping human, rat, mouse, fly, worm, dog, chicken, chimpanzee and yeast orthologs on maps and networks for pathway analysis solutions
• Password-protected individual and group accounts
• Import/export, store networks, maps and gene lists in different formats
• Comprehensive reports produced from the compare experiments workflow

System design & access

• Oracle database architecture
• Seamless compatibility with customer’s IT infrastructure for comprehensive data mining applications
• Web-based access or “behind-the-firewall” internal server installation
• Named user or concurrent licenses for pathway analysis