Data-mining and pathway analysis

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MetaCore is an integrated software suite for functional analysis of Next Generation Sequencing, variant, CNV, microarray, metabolic, SAGE, proteomics, siRNA, microRNA, and screening data. MetaCore is based on a high-quality, manually-curated database of:

Transcription factors, receptors, ligands, kinases, drugs, and endogenous metabolites as well as other molecular classes.

Species-specific directional interactions between protein-protein, protein-DNA and protein-RNA, drug targeting, and bioactive molecules and their effects.

Signaling and metabolic pathways represented on maps and Networks.

Rich ontologies for diseases and processes with hierarchical or graphic output.


  • Pathway analysis of ‘omics’ data for drug discovery
  • Knowledge mining of the database for hypothesis generation
  • Target and biomarker assessment and validation
  • Disease pathway modeling and investigation of causal mechanisms
  • Patient stratification, comprehensive comparison, and functional fingerprinting


  • Access to the unrivalled biological systems content contained within the MetaCore database
  • Robust data parsers and dynamic thresholding for comparative studies across any datasets
  • Interactome and topology tools that help avoid literature bias and rank molecular entities based on their connectivity for the dataset
  • Controlled vocabulary which provides one single semantic framework for all biological entities and their interactions
  • Rich proprietary ontologies that can be used for enrichment and functional profiling of multiple samples and various data types concurrently
  • Exporting and automated reporting capabilities that provide scientific workflow documents and network interactions and enrichments reports in minutes
  • Custom network building with flexible and powerful algorithms and tools for easy network analysis
  • Custom ontologies for user-made networks that can be used for enrichments
  • Custom maps for hypothesis visualization and collaborative research
  • Custom interactions that can be introduced and juxtaposed over existing MetaCore interactions

Technical Specifications

Client (For Web Portal and in-house installations):
Mac (PPC or Intel) or Windows P4 2GHz CPU and 1GB; RAM recommended Web browser; Internet Explorer version 6.0; Firefox 2.0; Safari 3.0.4 or higher; Macromedia Flash Player 8 or higher; Java Runtime Environment (JRE) 1.5.0
Server (for in-house installations):
2 or more P4/XEON CPU’s with 4GB of RAM recommended; 3.2 GHz CPU and higher recommended; SCSI HDD with minimum of 250GB of storage is recommended; RAID recommended; RedHat Enterprise Linux 3, 4or 5.1; SuSE 9.2; CentOS 4.4 X development package installed; Oracle 10.2 DBMS and client tools MetaCore supports x86-64bit architecture;

Product Add-ons

Data Annotation and Processing Tool

A user-friendly wizard that will manage, annotate, and statistically process our data in minutes.

Pathway Map Creator

A software tool for custom editing of existing canonical pathway maps, conversion of networks into map views for pathway analysis, and drawing regulatory and metabolic maps from scratch.


A knowledge base and data analysis module designed for the assessment of safety liabilities of drugs, environmental contaminants, and other xenobiotics at all stages of discovery and development.

The MetaCore™ Specialty Modules

Integrate pathology pathways maps for disease mechanisms, gene-disease associations (putative biomarkers), and small molecule and biologics therapies, along with an extensive OMICS data repository.

Systems Toxicology Module

Assess safety liabilities of drugs, environmental contaminants and other xenobiotics at all stages of discovery and development.