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If no majority exists, we select the most upstream gene start predicted.
Hence, Oct4 is considered to be the genetic "master switch" in the establishment of totipotency-pluripotency during the life cycle of mammals [ 23], and it is presumed to be the most upstream gene in the molecular circuitry of pluripotency [ 24].
The most upstream gene on a chromosome (where we represent the start and end sites of genes encoded on the antisense strand as their end and start sites on the sense strand, respectively), was assigned to the first imprinted cluster of that chromosome.
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ELF4 plays an important role in regulating the circadian activity and is the most upstream genes.
We note that most footprints of selection detected in this study involve the most upstream genes of the flowering pathway.
All potential outcomes appear possible, as these studies have found no relationship to pathway structure (Jovelin et al. 2009), a trend similar to that observed in metabolic pathways in which the most upstream genes evolve more slowly (Riley et al. 2003), and an inverse polarity in which the most downstream genes tend to be more conserved (Alvarez-Ponce et al. 2009, 2010; Wu et al. 2010).
Additionally, we analyzed the chromosomal location for each entry and identified any genes overlapping with this location, the most immediate upstream gene, and the most immediate downstream gene.
Further analyses are required to elucidate the most upstream causative gene of gastric cancer.
By using the murine Gnas imprinted domain, he demonstrated that truncating the most upstream Nesp gene, which is transcribed through the whole locus in oocytes, including across the two germline differentially mehtylated regions (DMRs), disrupts methylation acquisition at the DMRs.
To maintain a consistent approach to that used to construct the plant promoter set, we selected only the TSSs located the most upstream of genes.
Since in some imprinted clusters more than a single gene met this condition, we grouped all physically consecutive candidate cluster center genes to a single gene which start site was defined as the start site of the most upstream candidate center gene and end site was defined as the end site of the most downstream candidate center gene.
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Justyna Jupowicz-Kozak
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