Ubiquitination

Ubiquitination is a protein modification in which ubiquitin molecule covalently binds to the lysine residues of ubiquitin substrates (Hicke, 2001). This Two Sample Logo example contains 25 residue fragments, 12 upstream and 12 downstream, from all lysines found in 95 ubiquitinated proteins reported by (Hichcock et al., 2003) and (Peng et al., 2003). The positive sample contains 110 non-redundant fragments around experimentally verified ubiquitination sites, while the negative sample contains all remaining lysines from the same set of proteins, 2885 in total. In order to help answering a question about sequence biases around ubiquitination sites, a two sample logo can be generated to visualize residues that are significantly enriched or depleted in the set of ubiquitinated fragments.

Tyrosine Phosphorylation

Reversible protein phosphorylation provides a major regulatory mechanism in eukaryotic cells. At least one third of eukaryotic proteins is believed to be phosphorylated (Marks, 1996). This Two Sample Logo example contains 25 residue fragments, 12 upstream and 12 downstream, from all tyrosines found in 3408 phosphorylated proteins reported by (Iakoucheva et al., 2004). The positive sample contains 136 non-redundant fragments around experimentally verified phosphorylation sites, while the negative sample contains all remaining tyrosines from the same set of proteins, 5103 in total. In order to help answering a question about sequence biases around phosphorylation sites, a two sample logo can be generated to visualize residues that are significantly enriched or depleted in the set of phosphorylated fragments.