Normalize gene symbols
Use modern HGNC names for interpretation, but substitute old names when the frozen bundle requires them.
Atlas / Primary microcephaly
MCPH Intersection Atlas
A guided reconstruction of the inherited R protocol and the biology behind it. The atlas keeps the old bundle reproducible, explains the script from syntax to biological consequence, decodes the heatmap block by block, and updates the interpretation with current gene-symbol and database evidence.
Protocol map
From gene list to evidence matrix.
Load precomputed resources
Expression matrices, MAGMA gene-level p-values, GWAS gene lists, disease gene sets, and developmental slopes.
Intersect rows
Keep genes present in the bundle universe, then attach every available evidence layer to those rows.
Render heatmap
Compress the evidence into one row-aligned figure: expression timing, DV fold change, slope blocks, gene sets, MAGMA, and GWAS dots.
Alias decision for v2:
run the old protocol with
KNL1 -> CASC5 and TRAPPC14 -> C7orf43,
then label the rows with current HGNC-approved symbols.
Why this matters
The original script is not wrong because it uses old names; it is frozen in the naming
conventions and database snapshots of the project that produced it. The scientific risk
is different: if we feed it current symbols without an alias bridge, true MCPH genes
can disappear from the analysis. That happened with KNL1 and
TRAPPC14. A modern thesis-friendly analysis should therefore preserve two
symbol layers at the same time: the bundle-compatible symbol needed to reproduce the
old heatmap, and the current HGNC symbol needed to communicate the result correctly.
Script microscope
Line by line, expression by expression.
R script
Plot atlas
The heatmap is a stack of biological questions.
Gene profiles
Current MCPH list, ready for evidence expansion.
Database profiles