Tutorial Sheet
1. Using the Database of Interacting Proteins, identify interaction partners of a protein
involved in immune signaling (e.g., CXCR4). Describe how you would retrieve and
export the interaction data.
2. A researcher wants to study signaling proteins involved in cancer. Explain how you
would use the MINT database to obtain experimentally validated protein–protein
interactions.
3. If you are studying a human disease protein such as TP53, demonstrate how the Human
Protein Reference Database can be used to retrieve interacting proteins and associated
pathways.
4. Suppose you want to identify proteins interacting with a metabolic enzyme. Describe
how you would search the BioGRID database and download the interaction dataset.
5. A scientist is interested in experimentally validated protein interactions for inflammatory
pathways. Explain how IntAct can be used to filter interactions based on experimental
evidence.
6. Using the Reactome database, demonstrate how to identify pathways associated with a
given gene and visualize the molecular interactions involved.
7. If you identify a list of differentially expressed genes from an RNA-seq study, explain
how you would use Reactome to determine the biological pathways in which these genes
are involved.
8. You have identified a gene expression signature for a disease. Explain how the
Connectivity Map can be used to identify potential drugs that reverse this gene
expression pattern.
9. Describe how Connectivity Map can help in drug repurposing for diseases by
comparing gene expression profiles.
10. You have downloaded protein interaction data from BioGRID. Explain how you would
visualize and analyze the network using Cytoscape.
11. After constructing a protein interaction network in Cytoscape, describe how you would
identify hub proteins using network analysis tools.
12. If you want to explore the topology of a biological network visually, explain how Gephi
can be used to analyze network centrality and clustering.
13. You are given a dataset of protein–protein interactions. Describe how you would import
the data into Cytoscape and calculate network properties such as degree and clustering
coefficient.
14. A research group wants to compare different biological networks. Explain how Gephi
could be used to visualize network structures and detect communities or modules.
15. Suppose you identify protein interaction data from IntAct and pathway data from
Reactome. Describe how you would integrate these datasets and visualize them in
Cytoscape to study disease-associated pathways.
16. A systems biologist wants to identify drug targets in a signaling network. Explain how
protein interaction databases, pathway databases, and network analysis tools can be
combined to identify potential therapeutic targets.
Answers
1. Using DIP to identify interaction partners
Search the protein name or gene ID in Database of Interacting Proteins.
Steps:
1. Enter the protein name (e.g., CXCR4) in the search bar.
2. Open the protein entry.
3. View the list of interacting proteins and interaction evidence.
4. Download interaction data in available formats (e.g., tab-delimited or PSI-MI format).
2. Using MINT for experimentally validated interactions
In MINT:
1. Search for the protein name or UniProt ID.
2. Filter results based on experimental evidence.
3. View interaction partners and associated publications.
4. Export the dataset for network analysis.
3. Retrieving TP53 interactions from HPRD
Using Human Protein Reference Database:
1. Search for TP53.
2. Open the protein entry page.
3. Navigate to the protein–protein interaction section.
4. Retrieve interacting proteins and associated pathways.
4. Searching interactions in BioGRID
In BioGRID:
1. Enter the protein or gene name.
2. Select the organism (e.g., Homo sapiens).
3. Review interaction results.
4. Download interaction datasets in tab-separated or network formats.
5. Filtering interactions in IntAct
Using IntAct:
1. Search the protein of interest.
2. Apply filters for interaction detection method or experimental evidence.
3. Review curated interaction records.
4. Download interaction data for further analysis.
6. Identifying pathways in Reactome
In Reactome:
1. Search for the gene name.
2. Open the gene entry.
3. View associated pathways and reactions.
4. Use the pathway browser to visualize molecular interactions.
7. Pathway analysis of differentially expressed genes
Steps:
1. Upload the gene list to Reactome pathway analysis tool.
2. Perform enrichment analysis.
3. Identify significantly enriched pathways.
4. Interpret biological processes involved in the disease.
8. Using Connectivity Map to identify drugs
Using Connectivity Map:
1. Upload a gene expression signature (upregulated/downregulated genes).
2. Compare the signature with drug-induced expression profiles.
3. Identify compounds that reverse or mimic the disease signature.
9. Drug repurposing using Connectivity Map
Connectivity Map compares disease gene signatures with drug-induced profiles.
Drugs that reverse disease gene expression patterns may serve as potential therapeutic
candidates.
10. Visualizing BioGRID data in Cytoscape
Steps:
1. Download interaction data from BioGRID.
2. Import the file into Cytoscape.
3. Generate a protein interaction network.
4. Use layout algorithms to visualize the network.
11. Identifying hub proteins in Cytoscape
Steps:
1. Use network analysis tools in Cytoscape.
2. Calculate node degree and centrality metrics.
3. Proteins with the highest degree values are considered hub proteins.
12. Network analysis in Gephi
Using Gephi:
1. Import the interaction dataset.
2. Apply visualization layouts.
3. Run network statistics such as centrality and clustering coefficient.
4. Identify important nodes or clusters.
13. Calculating network properties in Cytoscape
Steps:
1. Import interaction data.
2. Run network analysis using Cytoscape tools.
3. Calculate parameters such as:
o degree centrality
o clustering coefficient
o shortest paths.
14. Detecting communities in Gephi
Steps:
1. Import the network into Gephi.
2. Use modularity detection algorithms.
3. Identify clusters or communities representing functional modules.
15. Integrating IntAct and Reactome data
Steps:
1. Retrieve interaction data from IntAct.
2. Obtain pathway information from Reactome.
3. Import both datasets into Cytoscape.
4. Map proteins onto pathways and visualize interaction networks.
16. Identifying drug targets using integrated analysis
Steps:
1. Collect protein interaction data from PPI databases.
2. Perform pathway enrichment analysis using Reactome.
3. Construct networks in Cytoscape.
4. Identify hub proteins or key pathway regulators as potential drug targets.