Sunday, July 28, 2013 7:27 AM updated by Xiang Chen

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Phosphorylation data for Homo sapiens from several data resources was collected ( 9-Oct-2012 ). The data contains 137153 experimental verified phosphorylation sites within 17297 phosphoproteins, in which 10384 phosphoproteins have experimental verified information for different subcellular localization. Furthermore, the data pertaining to subcellular localization was extracted from UniProt/Swiss-Prot database released on 9-Oct-2012. Sequence annotated with ambiguous or uncertain subcellular localization terms, such as “potential”, “probable”, “probably”, “maybe”, or “by similarly”, were excluded. In addition, the experimental verified subcellular localization information of corresponding kinases was also extracted. The following table lists numbers of phosphorylation proteins and corresponding kinases for different subcellular localization (Numbers in parentheses represent the unique phosphoproteins or kinases from specific subcellular localization).

Training Dataset Construction for Subcellular Model-We developed subcellular phosphorylation prediction models using the unique phosphorylation proteome of specific subcellular localization. Phosphorylation data of Homo sapiens for eight subcellular localizations which contained more than 50 known phosphoproteins, Cell membrane, Nucleus, Cytoplasm, Mitochondrion, Golgi apparatus, Endoplasmic reticulum, Secreted, Lysosome were used to construct the training datasets of the models. In this study, phosphorylation sites (positive training data) were represented as peptides of length 13, with the phosphorylated residue in the center and six amino acids on either side. When a particular phosphorylated residue was too close to the beginning or end of the protein to have six residues on either side, the missing residues were represented by “*” characters. The following table summarizes the training datasets for eight subcellular localizations and statistics for different phosphorylation types of the subcellular localizations (Numbers in parentheses represent unique proteins or residues after running the non-redundant dataset construction procedure with a sequence identity threshold of 30%.).

The experimental verified subcellular localization information of kinases was collected in human, you can download from here:

The names of all kinase and eight subcellular localization kinase were collected in human, you can download from here:

The names of three kinase type (serine, threonine and tyrosine kinase) in human, you can download from here:

The experimental verified subcellular localization information of phosphorylation substrates was collected, you can download from here:

The names of unique phosphoproteins from cell membrane can be downloaded from here:

The names of kinases from cell membrane can be downloaded from here:

The names of unique phosphoproteins from cytoplasm can be downloaded from here:

The names of kinases from cytoplasm can be downloaded from here:

The names of unique phosphoproteins from nucleus can be downloaded from here:

The names of kinases from nucleus can be downloaded from here:

The names of unique phosphoproteins from mitochondrion can be downloaded from here:

The names of kinases from mitochondrion can be downloaded from here:

The names of unique phosphoproteins from golgi apparatus can be downloaded from here:

The names of kinases from golgi apparatus can be downloaded from here:

The names of unique phosphoproteins from endoplasmic reticulum can be downloaded from here:

The names of kinases from endoplasmic reticulum can be downloaded from here:

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The names of unique phosphoproteins from secreted can be downloaded from here:

The names of kinases from secreted can be downloaded from here:

The names of unique phosphoproteins from lysosome can be downloaded from here:

The names of kinases from lysosome can be downloaded from here: