992 genes linked by the literature3,706 genes with papers179 clusters179 drawn (992 genes)modularity Q = 0.856
How to read this. Each dot is a cluster of genes that papers link, as named
partners or as members of the same complex. The label is the cluster's most-connected gene.
The colour is the most common hyperLOPIT localisation among the cluster's confidently
placed genes. Lines join each cluster to its strongest neighbours. Hover a dot for its
localisation, click it for its genes, and click a legend entry to highlight one group.
Literature-only, and incomplete by design. Links come from the partners and
complexes named in each gene's literature summary on this site, matched to gene cards by
name. This is not an interactome: no STRING, BioGRID or other network data is used. Two
clusters sit close because papers mention their genes together, not because the proteins
necessarily touch. Only genes with at least one matched link appear.
var (PfEMP1), rifin, stevor, PIR and SICAvar family
cards are left off the map: family members share one family-level summary, so a listed
"partner" is the same handful of names copied onto every member of the family, not
evidence about that specific card.
Colour = localisation
All clusters
The 179 clusters on the map, largest first. Hover a gene for its product and hyperLOPIT label.
Filters.
Non-coding RNA loci are left out, because rRNA/tRNA/snoRNA copies repeat the same finding.
var (PfEMP1), rifin, stevor, PIR and SICAvar family cards are left off the map by default (a switch on the builder can bring them back), because their partners come from one shared family-level summary rather than a per-card one.
When 8 or more genes sharing a product name all cite the same partner, those links are dropped as copies of one family member's findings.
The same rule removes such family members from a complex unless the complex name names them.
Localisation. hyperLOPIT calls for Pf3D7 genes from Chisholm et al. (2026)
Nature Communications 17:6192,
doi:10.1038/s41467-026-73664-2, via PlasmoDB build 71 (released 20 August 2026 00:00), dataset "Schizont spatial proteome (hyperLOPIT)".
The study assigns each gene to one of 24 compartments as a label, with no published
probability (unlike the Toxoplasma map's hyperLOPIT source) — the study's own calls are
grouped into eight colours here, and the exact compartment shows on hover.
"Not placed" marks a gene the study itself calls unknown; "Not in hyperLOPIT" marks a
gene with no Pf3D7 copy, or no row for it (Pb-only and Pk-only cards have no Pf3D7 gene).
Built 2026-09-11 from affinage_web_2026-09-11_patched.db by scripts/build_clusters.py.