Fig. 2: Gini Index unbiasedly identifies gene expression specific to embryonic craniofacial tissue genome-wide.

a Heatmap showing the specificity of expression for tissue-specific genes (rows) identified with high Gini scores (≥0.7) for all non-sex (n = 25) tissues (columns) from GTEx, embryonic heart, and fetal brain. Gene expression increases from light to dark. Embryonic craniofacial (blue), embryonic heart (red), and fetal brain (light green) specific genes and samples are highlighted, all other tissues are marked gray. b Selected significant (Benjamini and Hochberg–adjusted p value <0.05) disease ontology enrichments for genes identified to be specific for these tissues (Gini ≥0.7 and highest average expression). The dot size or count indicates the number of genes within a disease category. Color bars are log2 of the fold enrichment (see Methods). c Boxplots of gene expression of highest scoring Gini genes for the craniofacial tissues (n = 12) compared to embryonic heart (n = 24) and fetal brain (n = 5), of which all samples are biologically independent. The center line denotes the median value (50th percentile), the box contains the 25th to 75th percentiles and the whiskers mark the 5th and 95th percentiles. Data points beyond these values (outliers) are not shown. d Protein–protein interactions of 27 genes with conserved craniofacial expression bias in both humans and mouse as calculated by StringDB¹⁵⁵. The outer ring for each node indicates membership in MONARCH¹⁵⁶. Disease ontology categories were identified as significantly enriched in this gene set.