We assumed that SVD may establish some co-variations in gene expression that could enable better definition of expression-based functional alterations [8] [10].
In this paper, we introduce a global definition of expression context based on gene expression data.
According to the global definition of expression context introduced here, the expression correlation scores of all 1-1 orthologs in the genome add to the expression context.
At hour 0, under our definition of expression (CPM >1 in at least 50% of samples), 18,919 targets were detected forming the core transcriptome of the bovine dermal fibroblast under basal conditions.
Using the previous definition of expression where we require all replicates in a genotype to have FPKM values of at least 1, we identified 6,324 genes that were expressed in at least one genotype.
The exclusion criteria of studies also included (1) articles about cell lines or animals; (2) no definition of expression of CXCR4; (3) articles' lack of original data and control groups; (4) no relevant outcome data of OS or PFS; and (5) repetitive articles.
The global definition of expression context introduced here is based on the expression correlations between a query gene in one species and all the members in that species of all 1-1 orthologroupsroupresentent between the two species compared (see Fig. 1a).
Because of the particular nature of Russell's use of "contextual" definitions of expressions for classes, and the distinctive character of the theory of definite descriptions, he regularly called the expressions for such entities "incomplete symbols" and the entities themselves "logical fictions".
Other definitions of expression level, such as those weighing the experimental units with no expression, produced less defined picture [8], [9].
Before trying to answer this question, it is important to remember, that the level of resolution of our analysis was achieved considering the least correlated definitions of expression level and breadth.
