Genes found within these lab-specific candidate haplotype blocks are enriched for neurogenetic gene ontology categories along with functional classes related to regulation and behavior responses (Table 1) as well as other significant functional categories (Additional file 8: Table S4).
Keeping the above in mind, we find that DA blocks are enriched for TFBS turnover compared with non-DA blocks (P = 0.03, OR = 1.26 [95% CI, 1.02 1.55]; see row eight in table 3) and that the association of acceleration and turnover remains significant if we focus on DA blocks exclusively (FET: P = 3.12 × 10−5, OR = 11.00 [95% CI, 3.87 25.46]; see row nine in table 3).
In summary, we identified two independent effects within the BLK locus one of which covers the promoter region of the gene where the associated haplotype blocks are enriched for transcription factor binding sites for NFκB and IRF4, providing a potential mechanism for the correlation of the risk alleles and reduced levels of BLK expression.
Given that the DAPI-dense blocks are enriched for markers of constitutive heterochromatin, and that WSTF is involved in transcription [ 62], we assessed the WSTF mutant cells for changes in gene expression, with the thought that perhaps most gene expression changes would be reductions due to the gain in heterochromatin.
Additionally, genomic coordinates located upstream of blocking sites were enriched for thymine residues most likely resulting from the preferential capture of poly-A rich genomic regions by oligo-dT probes linked to the surface of the flow cell [ 10] (Additional file 1, Figure S2).
Hierarchical clustering of molecular profiles from IB4+SNS-Cre/TdT+, IB4−SNS-Cre/TdT+, and Parv-Cre/TdT+ neuron populations revealed a distinct segregation of these three DRG neuronal subsets, and large blocks of transcripts were enriched for each population (Heat-map, Figure 4A).
TFBS turnover DA blocks are enriched in many of the same GO terms as accelerated DA blocks, but lack the GPCR and olfactory receptor related terms (table 7).
The inoculated samples were enriched for 24 and 48 h.
Both reactors were enriched for "A.
These same fractions were enriched for endogenous RNAP-II.
