User Guide

Attribution

Code Repository:STARMAP software package,Code for accompanying paper

Please cite: Manuscript currently in preparation

Getting Started

The platform is organized around proteins, transcriptional regulatory networks (TRNs), and drugs.

  • Search for a protein to explore its structural organization and associated transcriptional and drug response patterns.
  • Search for a TRN to identify proteins associated with that transcriptional program.
  • Search for a drug to learn more about its structure and the protein regions it associates with.

Searching the Database

You can search the database by protein, transcriptional regulatory network (TRN), or drug using the search bar on the homepage. All searches are case-insensitive.

Protein Search

  • 3D protein structure view (AlphaFold or PDB), colored by structural region
  • 2D flatmaps highlighting spatial clustering of functional regions
  • Visualization of TRN associations mapped onto structure
  • Single-cell Perturb-seq validation of TRN associations
  • Single-cell drug perturbation validation of drug associations
  • Network view of similar proteins annotated with Gene Ontology terms

TRN (Transcriptional Regulatory Network) Search

  • Proteins most strongly associated with the selected TRN
  • Comparison to known STRING interactions between predicted proteins and TRN gene set members

Drug Search

  • PubMed and ChEMBL information for each drug
  • 2D flatmaps of proteins showing drug associations with specific structural regions

Downloads

Use this section to access underlying data for external analysis.

  • Protein-level scores and cluster assignments
  • TRN association matrices
  • Drug association results
  • Processed datasets used in STARMAP analyses

Interpreting Results

Structural regions represent spatially coherent areas of the protein associated with shared transcriptional or pharmacologic effects.

TRN and drug associations reflect statistically enriched patterns and should be interpreted as hypotheses for functional mechanisms rather than direct causal relationships.

Error Messages

If a query does not match any entry in the database, you will see:

"Sorry, we don't have information for [...]"

Data Sources

STARMAP combines data from the following sources:

Structural Data

  • AlphaFold Protein Structure Database
  • Protein Data Bank (PDB)

Mutation & Gene Expression Data

  • DepMap / Cancer Cell Line Encyclopedia (CCLE)

Protein Functional Annotation

  • UniProt

Protein–Protein Interaction Data

  • BioGRID
  • Interologous Interaction Database (IID)

TRN / Gene Set Data

  • Gene Transcription Regulation Database (GTRD) via MSigDB TFT collection

Single-Cell Perturbation Data

  • X-Atlas / Orion
  • Tahoe-100M

Drug Response Data

  • Cancer Therapeutics Research Portal (CTRP)

Variant Functional Effect Data

  • MaveDB