Methods and Compositions for Species-Specific Kinome Microarrays

摘要

A method of preparing a species-specific phosphorylation site peptide array for a target organism comprising: a) selecting a plurality of known non-target organism (NTO) phosphorylation site sequences and cognate known NTO phosphorylation polypeptide sequences from one or more NTO, each of the known NTO phosphorylation site sequences comprising at least 5 residues and less than 30 residues; b) identifying a matching target organism (TO) phosphorylation site sequence and cognate TO phosphorylation polypeptide sequence for one or more of the known NTO phosphorylation site sequences; c) determining the matching TO phosphorylation site sequences that correspond to orthologue polypeptides of the cognate known NTO phosphorylation polypeptide sequences; d) selecting the matching TO phosphorylation site sequences determined to correspond to orthologue polypeptides for inclusion on the array; wherein the matching TO phosphorylation site sequences that correspond to orthologue polypeptides are determined by calculating, for each matching phosphorylation site sequence identified in b), a similarity value between the TO phosphorylation polypeptide sequence corresponding to the TO phosphorylation site sequence and a TO polypeptide sequence matching the cognate known NTO polypeptide sequence.

主权项

1. A method of preparing one or more species-specific phosphorylation site database entries for a target organism comprising:
a) selecting a first known non-target organism (NTO) phosphorylation site sequence of a first non-target organism, the first known NTO phosphorylation site sequence comprising at least 5 residues and less than 30 residues; b) obtaining for the first known NTO phosphorylation site sequence a first cognate known NTO phosphorylation polypeptide sequence corresponding to the first known NTO phosphorylation site sequence, the cognate known NTO phosphorylation polypeptide sequence comprising the first known NTO phosphorylation site sequence; c) identifying a matching target organism (TO) phosphorylation site sequence for the first known NTO phosphorylation site sequence; d) obtaining for the matching TO phosphorylation site sequence a cognate TO phosphorylation polypeptide sequence corresponding to the matching TO phosphorylation site sequence, the cognate TO phosphorylation polypeptide sequence comprising the matching TO phosphorylation site sequence; e) determining a plurality of output values, each output value indicative of a degree of matching between the TO phosphorylation site sequence and the NTO phosphorylation site sequence; and f) determining a similarity value between the first known NTO phosphorylation polypeptide sequence and the cognate TO phosphorylation polypeptide sequence, wherein the similarity value provides an indication of whether the first known NTO phosphorylation polypeptide sequence and the cognate TO phosphorylation polypeptide sequence are orthologues of each other.