Exact(26)
The large confidence intervals associated with the larval/pupal stage are likely due to a reduced number of genes classified as specific to this stage, especially in the case of the higher specificity thresholds (Table 1).
The mean number of interactions was also higher for genes specific to the embryo as compared to the adult stage at most specificity thresholds (P < 0.05; Additional file 13).
In the case of the pooled embryonic gonads, under all specificity thresholds where the differences were statistically significant, genes classified as embryonic gonad specific are evolving less rapidly than whole embryonic tissue.
Genes were reclassified into developmental stages using a series of arbitrarily chosen specificity thresholds, such that in order for a gene to be classified as specific to a stage, its highest proportion of representation had to occur at that stage and also exceed the proportion of representation at any other stage by a threshold of more than twofold, fourfold, or eightfold.
Accordingly, jurisprudence relevant to processing situations with similar, or lower, specificity thresholds can be used to provide relevant points of comparison.
With lower specificity thresholds, gradually more patterns can be revealed, which carry progressively less information about stimuli.
Similar(34)
ChIP-qPCR is often used to determine in vitro whether a given ChIP-seq DNA fragment cluster belongs to a specific TFBS and, subsequently, to estimate the specificity threshold for the original ChIP-seq dataset by extrapolation.
Our probabilistic model shows that at the conventional specificity threshold % (> 95%), the fraction of high-avidity specific sequences and TF binding loci containing these sequences are surprisingly low in all studied libraries.
When adult gonads were separated into either ovary or testis-specific genes, only genes classified as testis specific had significantly fewer mean interactions (P < 0.05 at no specificity threshold and a greater than twofold proportion of representation threshold).
However, the control data provided many strong peaks which are often found in specific genomic regions like satellite repeats creating an unpredictable bias in identification of specificity threshold.
It is notable that only 5 of the 21 LII-specific genes previously identified by Doumith et al [ 10] passed our lineage specificity threshold.
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