Discovery of Protein Phosphorylation Motifs through Exploratory Data Analysis
Figure 2
Overview of motif finding steps.
In Step 1, for PCM we use the background data and foreground data, for PWM encoding, in place of the background data we use the entire Phospho.ELM database, while for binary encoding neither the foreground nor the background data are used. In Step 2 the k-means clustering algorithm is repeatedly used to generate a composite motif list (CML). This CML is then used to generate the final list of motifs in a stepwise manner ensuring two factors: statistical significance of the motif using a Binomial distribution based model, and frequency of occurrence of the motif in the present foreground data is at least M.