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) XML and SBML formats for molecular network data
Simple tab-delimited format for molecular interaction data import from KEGG, BIND, DIP, Science Signaling, GO and other leading pathway databases
Flexible tab-delimited format for microarray data import
Multiple microarray platforms including Affymetrix, Agilent and Amersham
