The unigenes were finally classified into 11 categories based on molecular function, and the two most overrepresented terms were binding (nucleotide binding, protein binding, chromatin binding) and catalysis (see Additional file 2).
The unigenes were finally classified into 24 categories based on molecular function, and the two most overrepresented groups were binding (other binding, protein binding, nucleic acid binding) and catalysis (catalytic activity, transferase activity, hydrolase activity, oxidoreductase activity).
For categories based on molecular function, the genes were finally classified into eight categories, as shown in Figure 5B; the three most overrepresented GO terms were binding (nucleotide binding, protein binding, chromatin binding), catalytic, and transcription regulators.
For genes having nonsense SNPs that would cause NMD (Table 8), the molecular functions that are most overrepresented included phosphorylation, ATP binding, iron/calcium ion binding, nucleotide/RNA binding and transporter activity.
The most overrepresented molecular function was nucleic acid binding, encompassing transcription factors and factors regulating nucleic acid stability.
Kunarso et al. (2010) identified LTR7/HERVH as one of the most overrepresented TEs seeding NANOG- and POU5F1-binding sites throughout the human genome.
Using MICRA we identified the E-box, CAGCTG, as the most overrepresented 6 mer in the regions of Asense binding (131% overrepresented using a conservation threshold of 0.6; see Supplementary Figure S6; Figure 3C).
An Ets-binding site is the second most overrepresented motif when comparing Jurkat versus erythroid cells and is also overrepresented in Jurkat peaks versus control sequences.
The most overrepresented motifs were E2F (5′-TGGCGCCA-3′); G-box (5′-G.GGGG-3′); a well-documented ApiAP2 binding motif (5′-TGCAT-3′), and an unknown motif (5′-[A/C] AACTA-3′).
