Part B: Public Repositories
Pathway data
- WikiPathways
- Reactome
- KEGG
- Pathway Commons (collection)
- Published Pathway Figures
Network data
- STRING
- IntAct
- NDEx (collection)
Sources of PPI Data
- Experimental Techniques High Throughput Low
Throughput
- Computational Techniques
- Public Repositories
Know what to look for. Know what you’re getting.
Finding Network Data
Where do I find the network?
There is no such thing!
There are hundreds of different interaction databases
It depends on your biological question and your analysis
plan,
But know what you are getting…..
Starting with a gene list……
Networks
Broad coverage / Lower resolution
- STRING (stringApp)
- NDEx (built-in)
- PSICQUIC (built-in)
- IntAct (IntAct App)
String
StringApp
STRING Settings
STRING Results
STRING Options
STRING Enrichment
NDEx
CyNDEx App
- Repository for biological network knowledge
- Organisations and individual scientists can deposit
- Use CyNDEx App to import/export networks
- Featured collections include:
- Pathway Interaction Database (NCI-PID)
- Cancer Cell Maps Initiative (CCMI)
- The NDEx Butler
- NetPath
PSICQUIC
PSI common query interface
PSICQUIC is included in the Cytoscape network search
tool:
IntAct
IntAct App
IntAct - Filters
- Can filter network by:
- MI Score
- Interaction detection method
- Participant detection method
- Host organism
- Expansion (e.g. spoke vs. matrix)
- Type (interaction type)
- Mutations (hides unmutated edges)
Pathways
Higher resolution / Limited coverage (~50% of genes)
- WikiPathways (WikiPathways App)
- Reactome (ReactomeFI App)
- Pathway Commons (CyPath2 App)
- KEGG (KEGGscape App)
WikiPathways
WikiPathways App
- Handmade pathway models
- Collaborative platform open to all researchers
- Thousands of pathways for dozens of species
Use the Network Search Tool to select a resource:
WikiPathways Search
WikiPathways Results
Pathway Database Apps
Cytoscape
Core Concepts
Cytoscape Apps!
apps.cytoscape.org
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