Features

  • MedScan Technology
    • Search and mine the literature
    • Extract interactions from the literature to a database
    • Build targeted data sets for organisms, tissues, conditions, etc.
Visualize pathways in color and according to cellular localization

Pathway Visualization

  • Graphical user interface for drawing, coloring, viewing, editing and annotation of pathway and relationship maps
  • Automatic layout algorithms revealing pathway organization
  • Publication-quality illustrations in all major image file formats
  • Export of pathways as clickable HTML or XML files

Pathway Analysis and Curation

  • Create your own pathways and produce publication quality graphics and diagrams
  • Optimize views by filtering, pathway expansion, and protein classification
  • Build pathways for gene lists imported from microarray and other experiments
  • Display specific upstream and downstream events
  • Find interaction paths among molecules, cell objects and processes
  • Determine and identify common targets and regulators for a group of proteins

Molecular Interaction Networks from the Literature

  • Analyze pathways with ResNet database, compiled from PubMed abstracts and articles
  • Access more than 1,000,000 facts of regulation, interaction and modification
  • Validate the facts by clicking on the link to an original sentence, abstract or source

Pathway Reconstruction Algorithms

  • "Build Pathway" is a powerful search tool with flexible options to navigate the network database and build pathways. Choose from multiple algorithms for assembling a pathway such as "find only direct interactions", "find shortest paths", "find common targets" or "find common regulators".
  • "Find relevant networks" - finds pathways related to a list of molecules
  • Find differentially expressed networks (pathways) for a microarray experiment.

Data Mining and Searches

  • Find all interacting molecules for a protein or other biological entity
  • Find all networks/pathways for a query protein
  • Use context and field-specific database searches
  • Filter to see only specific types of biological objects to be included in your pathway, such as proteins, complexes, small molecules, cellular processes etc.
  • Filter to see only specific types of biological interactions such as binding interactions, post-translational regulation, expression regulation, enzymatic activity, molecular synthesis, transport, and others.
  • Review original literature sources for every relation within a pathway via direct links to PubMed abstract and exact source sentence where each finding is referenced.

Import and Analysis of Gene & Protein Lists

  • Import/export gene and protein lists
  • Map gene lists on signaling and metabolic pathways, and GO groups
  • Build and analyze pathways from imported lists
  • Work with protein IDs, names or aliases from various sources: Unigene IDs, Accession Numbers, LocusLink, Swiss-Prot, Affymetrix GeneChip® IDs, Gene Names and Gene Symbols

Literature Mining

  • Use integrated MedScan software to extract biological interactions from scientific text
  • Mine PubMed and build pathways from extracted facts
  • Update pathways using data from recent publications

Microarray Gene Expression Data Analysis

  • Import data from all popular microarray analysis software packages
  • Reconstruct molecular networks from gene expression and proteomics data
  • View how genes in a pathway are up or down regulated through various biological states to identify key regulators or targets of interest

Supported Data Formats

  • ResNet Exchange (RNEF) and XML formats for molecular network data
  • Simple tab-delimited format for molecular interaction data import from GO and other leading pathway databases
  • Flexible tab-delimited format for microarray data import
  • Multiple microarray platforms including Affymetrix, Agilent and Illumina