Bio examples
Edit this page on GitHub →Every @basemark/bio directive, in one page. Rendered server-side to static HTML via renderMarkdownToHtml(), then upgraded client-side into real custom elements — the same two-step path every page on this site uses.
Protein sequence & structure
TCF7L2 (also called TCF-4), a Wnt-pathway transcription factor — its full-length domain architecture from UniProt, and the one crystallized structure of it bound to β-catenin.
The full TCF7L2 sequence (UniProt Q9NQB0), with its DNA-binding HMG-box domain and other annotated features laid out across the protein.
PDB entry 1JPW: the crystal structure of a fragment of TCF7L2 in complex with β-catenin, the interaction Wnt signaling actually turns on.
Variant cards (ClinVar/dbSNP)
Three variants, fetched live from MyVariant.info by rsID — one per ClinVar significance category, so the color coding actually shows something. First is the variant the locus-wide plots below are all about.
Genomic-locus plots (LocusZoom)
All six center on the same locus — TCF7L2, chr10:114,550,452-115,067,678 — the single most replicated genetic association in type 2 diabetes, led by intronic variant rs7903146.
The region GWAS meta-analyses actually plot: points colored by linkage disequilibrium with the lead variant.
Same association plot, with previously published GWAS Catalog hits labeled directly on it.
The 95% Bayesian credible set — the smallest set of variants 95% likely to contain the true causal one.
The same association points, plus a track of labeled genomic regions (e.g. chromatin states) beneath them.
Four related metabolic-trait GWAS (fasting glucose, fasting insulin, triglycerides, total cholesterol) layered on one panel.
The inverse view: rs7903146 (10:114758349_C/T) scanned across many phenotypes instead of many variants across one.
Genome browser (IGV.js)
A scrollable/zoomable view of raw genomic coordinates — distinct from the association plots above, which show a specific statistic, not "what's actually at this region."
Pathway diagram (KEGG)
TCF7L2 sits in the Wnt signaling pathway — the map below is the reference (species-agnostic) diagram for it.
Interaction network (STRING)
The same TCF7L2–β-catenin relationship from the structure tab above, now as a protein-protein interaction network instead of a 3D structure.
A single gene, with species left at its default (human, taxon 9606) — STRING expands it to its own top interaction partners automatically.
Same idea in mouse (taxon 10090) instead of human — the species attr is any NCBI taxonomy ID, not just the default.
Inline sequence & tree (Tier 3 — no fetch)
Short content the author supplies directly, parsed and rendered with no accession lookup. Directives, not fences — see Authoring syntax.
A short peptide, with residues 10-25 highlighted.
A small phylogenetic tree, branch lengths drawn to scale.
No branch lengths given at all — every branch falls back to equal spacing, so this renders as a pure cladogram (topology only, no evolutionary-distance meaning).
A slightly deeper tree, mixing very short (primate) and much longer (fish-vs-mammal) branch lengths in the same plot.