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Harvard PPI Visualization
Navigating the Dashboard
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This dashboard demonstrates the visualization of the events that were assembled by the Integrated Network and Dynamical Reasoning Assembler (INDRA). All the PPI events were divided into 16 categories (full list can be found here). Furthermore, from a high level, to enhance the biological understanding of the proteins involved in these events, we categorize the PPI events into 2 meta groups, namely Modification and RegulateActivity. Protein agents in Modification can be labeled as Subject protein or Object protein, while those in RegulateActivity can be labeled as Enzyme protein or Substrate protein.

Description of Visualization Pins

Containers Word Cloud

This word cloud shows the frequency of various gene/protein containers extracted from PPCA dataset. For example, apoptotic process Activator is a list of proteins that are found to be able to activate apoptotic process. Similarly, EIF2S1 Phosphorylator contains a list of proteins that are found to have phosphorylation with some other genes.

Enzymes Word Cloud

This word cloud shows the frequency of proteins that can be the enzymes in the Modification relation.

Subjects Word Cloud

This word cloud shows the frequency of proteins that can be the subjects in the RegulateActivity relation.

Subject-Object Interactions

This heat map shows the co-occurrence of subject and object proteins. For example, if we take the intersection block of the fourth row and second column, we can get DDX58 and Interferon. It means this pair of proteins can express one or more types of RegulateActivity relations.

Enzyme-Substrate Interactions

This heat map shows the co-occurrence of enzymes and substrate. For example, if we take the intersection block of the second row and first column, we can get EIF2AK2 and EIF2S1. It means this pair of proteins can express one or more types of Modification relations. The first row shows the frequency of Modification relations that have substrates only.

Subject-Object Interactions - Activation

This one is similar to Subject-Object Interactions except that the relation can only be Activation.

Subject-Object Interactions - Inhibition

This one is similar to Subject-Object Interactions except that the relation can only be Inhibition.

Container-Object Interactions

This heat map shows the co-occurrence of protein containers and subject proteins. For example, if we take the first column, it shows Interferon could be JAK activator and STAT Activator, etc.

Keyword - Journal Relations

This heat map shows the co-occurrence of a keyword in abstract with the journal names. For example, if our keyword is Coronavirus, we can get this keyword appears 149 times in articles published on PLoS One.

Authors Word Cloud

This word cloud shows the authors of the articles that have been archived into COVID-19 dataset.

Journal Publish Time Bar Chart

This bar chart shows the publish time of articles in each year and each month.

Interactive Navigation Examples

  • Click EIF2S1 Phosphorylator on Containers Word Cloud → Enzymes Word Cloud will tell you the members of this container → Keep adding more filters or clear for another navigation.
  • Click the intersection of Coronavirus and Virology in Keyword - Journal Relations → all the other pins will be updated. We can find David A. Brian from Authors Word Cloud, SARS-CoV Palmitoylators from Containers Word Cloud, etc. that are related to coronavirus.