PATHWAY STUDIO FEATURES
Pathway reconstruction, analysis and curation
Pathway visualization and publication-ready diagrams
High throughput data analysis
Literature mining
Supported data formats
Pathway Reconscruction, Analysis, and Curation
Pathway Studio uses functional relationship data from the ResNet database and intuitive network construction tools to help you build pathways from a single protein/gene/metabolite, a list of genes/proteins/metabolites, or from a complete high-throughput experiment:
- Find regulators to explain experimental data results
- Identify signal cascades that affect transcription
- Find drugs and small molecules known to effect specific gene or protein regulation
- Find genes and proteins with a causative or affected by specific diseases
- Build pathways from your literature search results using MedScan module
- Automatically update pathways with recently published information.
PATHWAY VISUALIZATION
Pathway Studio has the “best of breed” graphical interface for drawing, coloring, viewing, editing and annotating pathway diagrams and biological interaction maps. Specific features include:
- Automatic layout algorithms revealing pathway organization and cellular localization
- Publication-quality illustrations in all major image file formats
- Ability to annotate and fully customize presentation through user configurable styles.
- Export of pathways as clickable HTML or XML files
HIGH THROUGHPUT DATA ANALYSIS
Pathway Studio helps you get your data in, organize it, perform powerful analyses, and then visualize the results.
- Advanced network building and data analysis algorithms including Gene Set Enrichment Analysis (GSEA), Sub-network Enrichment Analysis, and Build Dense Expressed Networks,
- Ability to view multiple channels of experimental data, such as time/dose or proteomics / metabolomics combined.
- Easy importers for proprietary and generic experimental data such as Affymetrix CEL. Intelligent import wizard for GEO GDS.
- Flexibility and support for analysis of microRNA, SNP, exon data, phosphorylation, metabolomics, ChiP-on-chip, etc. Call Ariadne for more info.
- Sample Correlation Viewer helps to group samples and identify potential outliers
- Multiple Expression viewer displays multiple channels of experimental data on a network diagram
- Plug-ins available for direct export from some technology platforms.
LITERATURE MINING
Pathway Studio introduces a completely new way of literature mining, with ResNet database of functional relationships extracted from the whole publicly available literature, amenable for computational analysis.
- The results of literature mining are visualized as pathway diagrams
- You can update the ResNet database or create targeted datasets from published literature and internal text and PDF documents with MedScan module.
DATA SUPPORT
Pathway Studio can accommodate a wide variety of data for analysis. Ariadne’s ResNet Database is provided to Pathway Studio subscribers at no additional charge. Powerful import capability, and an open XML format (RNEF) facilitate the import and analysis of other data sets. Additionally, Pathway Studio includes direct compatibility for use of the following datasets:
- KEGG Pathways (requires appropriate end-user license)
- BioPax Pathways
- Prolexys Human Interactome database.
SUPPORTED DATA FORMATS
- ResNet Exchange (RNEF) XML and BioPax formats for molecular network data
- Simple tab-delimited format for molecular interaction data import from KEGG, BIND, Science Signaling, GO and other leading pathway databases
- Flexible tab-delimited format for microarray data import
- Multiple microarray platforms including Affymetrix, Agilent and Amersham
- Both raw and pre-processed microarray data
