For this analysis, we included a comparison with the Ubx binding sites identified by ChIP-chip experiments using 0 12 hour embryos, previously performed by the modENCODE project (www.modencode.org; see also the individual gene snapshots in Figures 4 and 5, which include an embryo Ubx binding track).
Next, we compared allelic ratios resulting from any of the three alignment methods (standard, IUPAC, allele-switch) to the single-gene SNaPshot measures of allelic expression (NuGen or GSP).
Therefore, we asked whether it is possible to identify subjects who will lose weight during dietary intervention using only a single gene expression snapshot.
While these studies may suggest that identifying predictive genes using a gene expression snapshot is possible, there are several critical differences between our work and these two aforementioned studies.
The aim of the present study was to assess whether a single gene expression snapshot prior to the 10 week consumption of a hypocaloric diet could be used to accurately predict whether an individual would lose weight or not.
While the degree of prediction accuracy currently achieved with a gene expression snapshot is perhaps insufficient for clinical use, this work reveals that the comprehensive molecular signature of adipose tissue paves the way for the future of personalized nutrition.
For this reason, considering only the gene expression snapshot of a single time point does not give a complete picture on the actual present proteome.
For each MEDLINE® Baseline release matched with Entrez Gene downloaded snapshot, we generated the MeSHOP for each disease in MeSH, the MeSHOP for each human gene using the associated GeneRIF annotation, and the MeSHOP for each human gene using the associated gene2pubmed annotation.
For this comparison, we individually measured allelic RNA expression ratios at 36 different SNPs in 21 genes using SNaPshot, for a total of 186 comparisons across the 9 tissues (Additional file 4: Table S3).
Each element X ut corresponds to the expression of gene u at snapshot t.
