Welcome to the scnbase PROTEIPEDIA for the soybean cyst nematode, Heterodera glycines!
This interface lets you browse and filter candidate effectors in dynamic tables and learn the patterns or insights from interactive visualizations.How to get started?
Just use the Search box to look up features (transcripts) by ID or click on Proteipedia to explore putative SCN effectors within sortable tables, apply on-the-fly filters and use links to detailed protein pages.
Features
Each candidate effector protein in the resource is annotated with multiple classes of information:
- Core information: organism, feature ID, protein length, sequence
- Secretion prediction: signal peptide score (SignalP5/6) and ranges, secretion consensus, transmembrane domains
- Structural annotation: predicted globular domains (Iupred2A), PDB hits, predicted disordered regions
- Biophysical properties: molecular weight, total charge, isoelectric point, amino-acid composition (charged, aromatic, basic/acidic, cysteine enrichment)
- Expression: stage-specific average gene counts (e.g. Egg, J2, J3, J4, female, male) and log2 fold-changes key biological contrasts (sex, life stages, gland vs body, line comparisons)
Visual Interactive Exploration
The SCN Effector Atlas includes several visualization tools for exploratory data analysis:
- Summary plots: distributions of protein length, SignalP score, disorder, composition and other core properties
- Expression plots: stage-wise boxplots and mean expression profiles across the H. glycines life cycle
- Custom EDA: build your own scatterplots and histograms by choosing any annotated property on the X/Y axes, with points labeled by feature ID.