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Genes harboring these binding sites were classified as ERα-regulated genes that belonged to the luminal B breast cancer subtype (Table 1).
The midpoint of ESR1 binding sites were classified as falling within exons, introns, UTR, up-/down-/up&down-stream (5 kb) or intergenic regions relative to RefSeq genes.
To explore the relationship between sequence conservation and mode of AR regulation, binding sites were classified in a binary fashion as conserved or non-conserved based on summit position.
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This assures that all of the observed binding sites are classified correctly and the FP (FN) sites are those that are misclassified because they score higher (lower) than the cutoff although their true binding affinity is lower (higher) than the cutoff.
Thus, if the DNA methylation level at the 12th position of a CTCF binding site was found to be greater than 20%% [ 36], this binding site would be classified as "methylated" otherwise the binding site is classified as "unmethylated".
Smo drugs that occupy this 'cyclopamine binding site' are classified as such by their ability to compete with cyclopamine for Smo binding.
Next, each Eσ-binding site was classified into one of three categories depending on the number of σ-factors recruited to that site: single Eσ-binding promoter region (SPR), overlapped Eσ-binding promoter region (OPR), and intensively overlapped Eσ-binding promoter region (IOPR).
All the remaining sites were classified as non-14-3-3-binding non-14-3-3-binding non-14-3-3-binding non-14-3-3-binding non-14-3-3-binding
Sites were classified as non-neoplastic (normal, hyperplastic) and preneoplastic.
The sites are classified as 'new' or 'closed'closed
Cancers of unknown primary site were classified as Miscellaneous.
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CEO of Professional Science Editing for Scientists @ prosciediting.com