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We show how highly mutated domain peaks can be missed by gene-centric methods when the individual genes containing the domains are not mutated at high frequencies.
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Many individual genes contained binding sites for several of the homeobox transcription factors (Table S6).
Each QTL could contain many genes, but as the density of marker coverage improves it may be possible to narrow these QTL until it becomes feasible to characterise the individual genes contained within them.
The numbers refer to the individual candidate genes containing the different snoRNA structures as well as their total and the number of putative genes per 100 bp of target sequence used.
The full list of KEGG and GO annotations in GO-Elite showed that of the whole mouse genome represented on the arrays, 5699 individual genes were contained within the GO-elite KEGG database and 17730 individual genes were contained within the GO-elite GO database, and were used for analysis.
Using bioinformatics approaches, computational studies have documented valuable TF repertoires by searching for genes containing DBDs within individual organisms ranging from prokaryotes to eukaryotes or by searching across all completely sequenced genomes.
Individual genes also contain a limited number of nucleotide sites and therefore limited resolution.
1,499 individual genes were contained within the Ingenuity database and were used for analysis.
For the 33 core OCT4 target genes, Figure 6 lists the individual genes that contain the discovered motifs within their promoter regions.
The individual genes that contains SNPs were provided in additional file 1. Table 1 specifies the number of different SNPs identifying certain isolates.
However, this finding would not detract from the findings and the value of this study, i.e., demonstrating that individual genes frequently contain too little information to decide between alternative phylogenies.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com