Bioinformatics insights
TissueEnrich with custom reference datasets
Custom expression references can extend tissue-specific gene enrichment to specialized tissues, rare cell types, and experimental systems.
When public references are not enough
GTEx and other public resources are powerful, but they may not represent a specialized tissue, developmental stage, rare cell type, or model system. A custom reference can make enrichment more relevant to the biological question.
Build a comparable matrix
Begin with a well-documented expression matrix whose samples or groups are comparable. Harmonize identifiers, address duplicated genes, review normalization, and confirm that group labels reflect the intended biological categories.
Define specificity transparently
Tissue-specific classifications depend on relative expression thresholds and group coverage. Record these settings and inspect known markers to confirm that the custom reference behaves as expected.
Interpret enrichment in context
Enrichment indicates that a gene set overlaps a tissue-specific signature more than expected. It does not by itself establish causality, cellular origin, or disease mechanism; results should be integrated with the study design and orthogonal evidence.