Gene Pair Metrics
The total number of unique gene pairs where one gene (nested) is completely contained within another gene (host).
Host Genes
Genes that contain at least one nested gene within their boundaries.
Nested Genes
Genes that are found completely within the boundaries of other genes.
True Nested Genes
Intronic or exonic overlap nested genes - represents genes that truly fit the nested gene definition.
Nested Gene
A gene that is located entirely within another gene (the host gene), including being located within its introns.
Host Gene
A gene that contains another gene (the nested gene) within its genomic boundaries.
Intronic Nested Gene
A nested gene that is located entirely within the introns of its host gene.
Exonic Overlap
When a nested gene overlaps with the exons of its host gene, potentially affecting protein coding regions.
TSS/TTS Overlap
When the transcription start site (TSS) or transcription termination site (TTS) of one gene overlaps with another gene.
Complex Overlap
Multiple or complex patterns of gene overlap, potentially involving more than two genes or multiple overlap types.
Strand Relationship
The relative orientation (sense/antisense) of nested genes compared to their host genes.
Gene Density
The number of genes per unit length of genomic sequence, which can affect nesting frequency.
GTF/GFF Files
Standard file formats used to describe gene features in genomic sequences, including gene locations and structures.
Nesting Frequency
The proportion of genes in a genome that are nested within other genes.
Gene Structure
The organization of a gene, including exons, introns, and regulatory regions.
Genome Assembly
A specific version of a genome's DNA sequence, used as reference for gene identification and analysis.