Documentation PlantQTLdb Assistant Network Analysis with STRING
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Getting Started with Assistant Gene Structure and Sequence Extraction Variant Annotation and Local QTL Evidence Functional Enrichment with g:Profiler Network Analysis with STRING Finding Sequencing Data with ENA Sequence Similarity Search with BLAST Plant Motif Analysis with JASPAR and FIMO DNA Analysis with Evo2 External Biological Evidence Sources Troubleshooting and Limitations

PlantQTLdb Assistant

Network Analysis with STRING

explore functional associations or physical interaction evidence between candidate proteins

Requires Research mode

Open PlantQTLdb Assistant

When to use it

Ask whether 2–50 genes or proteins from one species have supported relationships. Input IDs are mapped to STRING proteins; ambiguous mappings require clarification rather than a guessed match.

How to ask and what you receive

Functional association network

ask
Use STRING to analyze the functional association network of Arabidopsis genes AT1G01010 and AT1G01020

what you receive

A STRING result card containing a network, mapped nodes and association scores, with JSON, CSV and SVG downloads. Verification returned two nodes and one edge for this input.

Request the physical network

ask
Use STRING to analyze the physical interaction network of Arabidopsis genes AT1G01010 and AT1G01020

what you receive

The physical-network query for the same mapped proteins. It may contain fewer edges or none; a functional-network edge does not guarantee a physical-network edge.

Actual STRING functional network result card with two proteins and one association
Production verification, 12 September 2026: two mapped proteins and one functional association.

Interpret the diagram

Functional association
Evidence that proteins participate in related biological processes; not necessarily direct binding.
Physical network
Physical-interaction evidence as represented by STRING, which can include membership in a complex; do not assume every edge proves direct binding.
Score and layout
Edge width follows confidence. The default threshold is 700/1000. Circular node positions have no biological distance meaning.

If the expected card does not appear

Confirm Research mode and resend the question. A literature answer without a STRING card does not demonstrate that the STRING analysis ran.

For a successful query with no edges, inspect mapping and the score threshold. Missing IDs or absent edges are not proof of no interaction. The tool uses STRING 12.0, does not automatically add neighboring proteins and returns at most 1,500 edges.