Can the protein interaction strength information chart show which protein is upstream and which is downstream?

Protein interaction intensity maps usually cannot directly display the upstream and downstream relationships between proteins, meaning they do not directly provide information on causal or regulatory relationships. These maps typically only show the existence of interactions between proteins and the strength of these interactions (such as affinity, binding constants, etc.).

 

To identify the upstream and downstream relationships between proteins, you may consider the following methods:

• Phosphorylation or post-translational modification analysis: Detect changes in protein phosphorylation after the action of specific signaling molecules to determine upstream and downstream relationships.

• Time series experiments: Observe the activation sequence of proteins at different time points to infer the direction of signal flow.

• Genetic or molecular interference experiments: Use gene knockout, knockdown, or inhibitor experiments to observe the response of downstream proteins.

• Signal pathway databases: Use bioinformatics databases like KEGG and Reactome to query existing signaling pathway information and understand which proteins have already been identified in upstream and downstream relationships.

 

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