Data from: Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifs

van Wijk KJ, Friso G, Walther D, Schulze WX

Date Published: June 13, 2014

DOI: http://dx.doi.org/10.5061/dryad.sb669

 

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Title Supplemental Data Set 1. Detailed overview of the 27 published p-proteomics studies and unpublished in-house data with their respective metadata.
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Title Supplemental Data Set 2. The complete unfiltered set of 60366 p-peptides with matched protein id, their metadata, p-15-mers, annotation from PPDB, SUBA3 consensus prediction and assignment to one of seven locations.
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Title Supplemental Data Set 3. Non-redundant Arabidopsis p-proteins before filtering (8141 proteins) or after filters 1&2 (set A – 4494 proteins) and after filters 1,2,3,4 (set B -3687 proteins) with their annotations.
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Title Supplemental Data Set 4. Non-redundant p-15-mers prior to filtering and for sets A and B.
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Title Supplemental Data Set 5A,B. Analysis of pY peptides (A) and pY proteins (B).
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Title Supplemental Data Set 6. Published plant p-motifs in various plant species based on motif-x searches against p-proteomics data.
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Title Supplemental Data Set 7. P-motifs for pS, pT and pY and their fold-enrichment in sets A and B, and the localization of p-15-mer sets using motif-x at the 10-6 threshold and 1%, 3% and 5% occurrence rates.
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Title Supplemental Data Set 8. P-motifs for pS, pT and pY in sets A and B and the localization of p-15-mer sets using MMFPh at the 10-6 threshold and 1%, 5% and 10% occurrence rates.
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Title Supplemental Data Set 9. Motifs for pS, pT and pY found by motif-x and MMFPh for sets A and B and subcellular sets at all occurrence thresholds
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Title Supplemental Data Set 10. P-proteins with their p-15-mers and their most significant motifs (from Table 2).
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Title Supplemental Figure 1A. Hierarchical clustering (average linkage method) of all 364 non-redundant pS motifs identified by motif-x and/or MMFPh in sets A, B and the subcellular sets.
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Title Supplemental Figure 1B. Hierarchical clustering (average linkage method) of all 26 non-redundant pT motifs identified by motif-x and/or MMFPh in sets A, B and the subcellular sets.
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Title Supplemental Figure 2. Kinase recognition motifs for different kinase families in Arabidopsis.
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When using this data, please cite the original publication:

van Wijk KJ, Friso G, Walther D, Schulze WX (2014) Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifs. The Plant Cell 26(6): 2367-2389. http://dx.doi.org/10.1105/tpc.114.125815

Additionally, please cite the Dryad data package:

van Wijk KJ, Friso G, Walther D, Schulze WX (2014) Data from: Meta-analysis of Arabidopsis thaliana phospho-proteomics data reveals compartmentalization of phosphorylation motifs. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.sb669
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