Sentence examples for marks we calculated from inspiring English sources
To quantify expression levels and the strength of KAP1 and SETDB1 marks, we calculated reads per kilobase per million mapped reads (RPKM) [ 77, 78] for genomic regions of interest.
Further to confirm that H3K36me2 is a global repressive mark, we calculated the correlation between transcription level and histone marks after the exclusion of virulence genes (first three subsets in Fig. 3a, which are also enriched with H3K9me3).
Based on mark-resight analyses, we calculated that 72% of adult males and 14% of banded nestlings returned to the study site in a following year.
To assess the strength of association between epigenetic marks (or mark interactions) with p65 binding we calculated enrichment p-values via the random set (RS) statistical test [ 73].
Although many packs have more than two wolves marked with VHF collars, we calculated attendance rates for two randomly selected individuals from each pack for each early-winter and late-winter study period (see Table S1).
We calculated the average marks for semester 1 (S1) and semester 2 (separatelytely.
The first use case is that of aggregate coverage profiles: given ChiP-Seq data, e.g. from histone marks, we want to calculate the profile of these marks with respect to specific positions in the genome, such as transcription start sites (TSSs), by aligning coverage data in windows centred on the TSSs and averaging over the TSSs of all genes or a subset thereof.
Correlations between scaled epigenetic marks were calculated as Spearman's rank correlation coefficient.
Overlaps between RTSSs and chromatin marks were calculated for each mark individually using downloaded enrichment peak-profiles from ENCODE (filename extension.broadPeak for histone modifications and histone variant H2A.Z and.narrowPeak for DNase HS).
To achieve quantitative analysis of epigenetic modifications, total signal intensities of epigenetic marks were calculated as follows: 1) All negative intensity values were considered as zero.
Profiles around each of the 179 369 globally defined RTSSs in each cell line for all chromatin marks were calculated from ChIP-Seq mapped sequence read libraries downloaded from ENCODE.
