In cases where adjacent acceptor residues precluded a definite assignment of phosphorylation locus, multiple candidate phosphorylation sites were reported.
In many gene promoters it is possible to find multiple candidate binding sites for any particular transcription factor.
Although multiple candidate TCF binding sites can be identified in the individual mouse or human fascin-1 promoter sequences ([3], [8]; our observations), phylogenomic analysis of conserved motifs demonstrates that, in fact, only one TCF site is conserved between primates and mice.
Multiple candidate regions as sites for Schizophrenia and Bipolar susceptibility genes have been reported, suggesting heterogeneity of susceptibility genes or oligogenic inheritance.
Overall, multiple candidate transcription factor binding sites were identified that met these criteria (Fig. 4A).
Beausoleil et al. (2006) report a probabilistic method that calculates an Ascore based on the appearance of phosphorylation sites in multiple candidate solutions to the spectrum-database mapping conundrum.
Grothey et al. [3] identified multiple candidate T cell factor (TCF) binding sites in the (mouse) Fscn1 promoter, but found no effect of either TCF or β-catenin over-expression on Fscn1 promoter activity when tested in human MDA-MB-435 cells.
(a) The frontal-affinity-chromatography technique has ideal efficiency, but requires affinity columns of short life-times and exhibits low reliability to judge the binding site(s) of multiple candidate ligands of unknown concentration in a mixture under analysis[ 10, 11].
Multiple alignment of the gene sequences containing the candidate sites was further checked.
Nonetheless, only a small fraction of these sites contained multiple variants, thus explaining why the number of candidate sites dropped so substantially upon the integrated application of steps 3 and 4. At step 6, a minimum read count filter was applied alone to assure that any particular variant (at a given site) was present in at least three reads.
