Skip to content

PPI — Protein-Protein Interaction Network

Header: PPI: Protein-Protein Interaction Network

The PPI tab visualizes protein-protein interactions among your significant differentially expressed genes using the STRING database. This helps identify functional relationships, protein complexes, and hub genes in your dataset.

How It Works

  1. Your significant DEGs (filtered by p-value and fold change thresholds) are sent to the STRING API
  2. Gene IDs are mapped to STRING protein identifiers
  3. Known and predicted protein interactions are retrieved
  4. Results are displayed as an interactive network graph

Note

This report requires an internet connection to query the STRING database. No pre-computed data files are needed — everything is computed on-the-fly from your DESeq2 results.

PPI-Specific Controls

Organism

A text input for the species name. The organism is auto-detected from your gene IDs and validated against STRING. For non-model organisms not in STRING (e.g., sweet potato), a compatible model organism is automatically suggested (e.g., Arabidopsis thaliana). If not detected, enter the full Latin name (e.g., Homo sapiens, Mus musculus, Arabidopsis thaliana).

Min Confidence

A slider to set the minimum STRING interaction confidence score:

Level Score Description
Low 150 Includes speculative interactions
Medium 400 Default — balanced coverage and reliability
High 700 Only well-supported interactions
Highest 900 Only highest-confidence interactions

Max DEGs

A slider (10–500, default: 100) controlling how many top significant DEGs to include in the network query. DEGs with resolvable gene symbols are prioritised to maximise STRING matches. Increase this value for non-model organisms where fewer genes have known symbols.

Network Graph

The main visualization is an interactive network where:

  • Nodes = proteins (your DEGs)
  • Edges = known or predicted interactions from STRING
  • Node color: red = upregulated, blue = downregulated, grey = other (uses sidebar Up/Down/Others colors)
  • Node size: scales from the sidebar Dot Size setting, growing with the number of connections (degree)
  • Node labels: use the sidebar Font color setting
  • Edge lines: use the sidebar Threshold line color setting
  • Color legend: displayed on the right side of the graph, showing Up-regulated, Down-regulated, and Other categories. Click a legend entry to toggle that group's visibility.

Hover over any node to see the protein name, log2 fold change, adjusted p-value, and connection count.

Hub Genes Table

An expandable table ranked by connectivity (number of interactions). Hub genes — those with the most connections — are often functionally important regulators. Columns include:

  • Protein — STRING preferred name
  • Connections — Number of interactions in the network
  • Direction — Up or Down regulation
  • log2FC — Log2 fold change
  • padj — Adjusted p-value

Interaction Table

An expandable table listing all pairwise protein interactions with individual evidence scores:

  • score — Combined STRING confidence score
  • nscore — Neighbourhood score
  • fscore — Fusion score
  • pscore — Phylogenetic profile score
  • ascore — Co-expression score
  • escore — Experimental score
  • dscore — Database score
  • tscore — Text-mining score

STRING Functional Enrichment

An expandable table showing functional enrichment results computed by STRING, including GO terms, KEGG pathways, and other annotation categories enriched among your queried proteins.