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The first row are four groups with interval of genes number.
Figure 2D marks the interval of genes involved in immune response and the associated reorganization of actin cytoskeleton.
These results show that a substantial proportion of human enhancers (36/192) reside within the intronic interval of genes they regulate (intragenic).
For example, if the annotated interval of genes in the zebra finch genome was expanded by 2,000 bp upstream and downstream then alignments of willow warbler reads overlapped with an additional 1,703 annotated genes.
In the integration interval of genes and QTLs, the gene transcripts were significantly A-subgenome biased, and the QTLs associated with fiber qualities were detected in corresponding A-subgenome chromosome bins.
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Then, by dividing frequency of positive gene sets by that of input gene set, we calculated relative performance of each method in each interval of gene set size (Table 1).
If a PHOG contains paralogs, the PHOG database indicates the probable timing interval of gene duplication events for all PHOGs that contain paralogs.
The resulting myelopoiesis expression data matrix included 9,425 genes, each reliably associated to a unique genomic position, identified as the bp interval of gene span, and to a single expression vector (Additional file 1).
It is often assumed that cis-acting regulatory sites act on the nearest neighboring genes and therefore the conventional search space for enhancers includes immediate upstream or downstream intervals of genes of interest.
L′ = L2 ∪ L V. L2 ⊆ L is the set of genes with two copies in T, and L V is a set of 'virtual' genes, each one representing a triple of intervals of genes (in L), (I1, I2, I3), the first, I1, on a chromosome in D, the second and third on chromosomes in T, such that I2 ∩ I3 = ∅, I2 ∪ I3 = I1.
In general, the mean enrichment formula is: enrichment = 50 / (rank), for an interval of 100 genes [ 40].
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com