Interpreting Results from Proteome-Wide PPI Inference

What follows is some guidance on how to interpret the results obtained by running proteome-wide PPI inference experiments using the PPI.bio website.

For instructions on how to conduct proteome-wide PPI inference experiments using this website, please see our "How-To Guide for Proteome-Wide PPI Inference".

Once the experiment has been computed and you the completed Proteome Prediction Report is shown, you will be presented with four tabs:

• Prob. Table - A datatable of all the inferred interactions between your submitted protein and the proteins on each row of the datatable.
• Prob. Histogram - A histogram showing the distribution of inferred interaction probabilities.
• GO Enrichment - A page which allows users to perform statistical over-representation experiments via PANTHER.
• GO Frequency - A histogram showing the distribution of GO term frequencies.

Probability Table

The first tab available to you is the Probability Table. This tab displays a table of all the inferred protein interactions and their score. Each row describes an inferred reaction between the protein whose sequence you've supplied and a protein in the proteome of the organism you've selected.

The meaning of each column is described below:

UniProt AC

The UniProt Accession of a protein in the proteome of the organism you've selected. This row reports the probability of interaction between the protein you've submitted and this protein.

Gene Name

The gene name of a protein in the proteome of the organism you've selected. It corresponds to the protein indicated by the UniProt Accession code in "UniProt AC". This row reports the probability of interaction between the protein you've submitted and this protein.

Protein Name

The protein name of a protein in the proteome of the organism you've selected. It corresponds to the protein indicated by the UniProt Accession code in "UniProt AC". This row reports the probability of interaction between the protein you've submitted and this protein.

Interaction Probability

Indicates the probability of interaction between the protein submitted and the protein indicated by the UniProt Accession code in "UniProt AC", as well as the other identifiers in this row. See the threshold guidelines for advice on interpreting these scores.

Probability Histogram

The probability histogram page shows the distribution of the inferred interaction probabilities. The x-axis reports the bins in which the scores are sorted into. They increase by intervals of 0.1 ranging from 0 to 1 inclusively. The y-axis shows the number of interactions in each bin.

GO Enrichment

The GO Enrichment page uses the PANTHER API to conduct a statistical over-representation test for Gene Ontology terms.

Below is a description of each field:

• Threshold - Interactions which have inferred probabilities of interaction below this score are not included in the analysis.
• Annotation dataset - Which set of Gene Ontology annotations to check for over-representation. Learn more about Gene Ontology Annotation datasets.
• Enrichment test type - Which statistical test to use in the analysis. Please see this article for guidance.
• Correction - Which method to use for p value correction. Please see this article for guidance.

To learn more about PANTHER, please refer to this manuscript in Nature Protocols and the PANTHER Help pages.