ArticleThe Plant cell2014
Meta-Analysis of Arabidopsis thaliana Phospho-Proteomics Data Reveals Compartmentalization of Phosphorylation Motifs.
Article in The Plant cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transcriptomic meta-analysis to identify potential antifungal targets in Candida albicans.BMC microbiology · 2024Pooled it
- Cross-Species Analysis of ABA-Induced Phosphosignaling Landscapes in Rice, Soybean, and Arabidopsis.Proteomes · 2026Article
- Proteome and Phosphoproteome of Tomato Fruit Identify REDUCED CHLOROPLAST COVERAGE 1a as A Ripening Regulator.Genomics, proteomics & bioinformatics · 2025Article
- Phosphoproteomic Analysis of Maize Seedlings Provides Insights into the Mechanisms of Heat-Stress Tolerance.International journal of molecular sciences · 2025Article
- Searching for Sulfotyrosines (sY) in a HA(pY)STACK.Journal of proteome research · 2025Article
- PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals.Cell reports methods · 2024Article
- Phosphorylation activates master growth regulator DELLA by promoting histone H2A binding at chromatin in Arabidopsis.Nature communications · 2024Article
- Quantitative phosphoproteomics reveals molecular pathway network in wheat resistance to stripe rust.Stress biology · 2024Article
- DNA-encoded probe-based assay for profiling plant kinase activities.PNAS nexus · 2024Article
- DecodingPlants (Basel, Switzerland) · 2024Article
- The cAMP-dependent phosphorylation footprint in response to heat stress.Plant cell reports · 2024Article
- Genetic analysis and QTL mapping for pericarp thickness in maize (Zea mays L.).BMC plant biology · 2024Article
- Large-scale analysis of the N-terminal regulatory elements of the kinase domain in plant Receptor-like kinase family.BMC plant biology · 2024Article
- Chilling stress response in tobacco seedlings: insights from transcriptome, proteome, and phosphoproteome analyses.Frontiers in plant science · 2024Article
- Transcriptional and post-translational regulation of plant autophagy.Journal of experimental botany · 2023Review
- Genome-Wide Identification and Characterization of thePlants (Basel, Switzerland) · 2023Article
- Protein-Protein Interactions and Quantitative Phosphoproteomic Analysis Reveal Potential Mitochondrial Substrates of Protein Phosphatase 2A-B'ζ Holoenzyme.Plants (Basel, Switzerland) · 2023Article
- Glycine-Induced Phosphorylation Plays a Pivotal Role in Energy Metabolism in Roots and Amino Acid Metabolism in Leaves of Tea Plant.Foods (Basel, Switzerland) · 2023Article
- Shared and unique phosphoproteomics responses in skeletal muscle from exercise models and in hyperammonemic myotubes.iScience · 2022Article
- Sucrose nonfermenting-1-related protein kinase 1 regulates sheath-to-panicle transport of nonstructural carbohydrates during rice grain filling.Plant physiology · 2022Article
30 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein (de)phosphorylation plays an important role in plants. To provide a robust foundation for subcellular phosphorylation signaling network analysis and kinase-substrate relationships, we performed a meta-analysis of 27 published and unpublished in-house mass spectrometry-based phospho-proteome data sets for Arabidopsis thaliana covering a range of processes, (non)photosynthetic tissue types, and cell cultures. This resulted in an assembly of 60,366 phospho-peptides matching to 8141 nonredundant proteins. Filtering the data for quality and consistency generated a set of medium and a set of high confidence phospho-proteins and their assigned phospho-sites. The relation between single and multiphosphorylated peptides is discussed. The distribution of p-proteins across cellular functions and subcellular compartments was determined and showed overrepresentation of protein kinases. Extensive differences in frequency of pY were found between individual studies due to proteomics and mass spectrometry workflows. Interestingly, pY was underrepresented in peroxisomes but overrepresented in mitochondria. Using motif-finding algorithms motif-x and MMFPh at high stringency, we identified compartmentalization of phosphorylation motifs likely reflecting localized kinase activity. The filtering of the data assembly improved signal/noise ratio for such motifs. Identified motifs were linked to kinases through (bioinformatic) enrichment analysis. This study also provides insight into the challenges/pitfalls of using large-scale phospho-proteomic data sets to nonexperts.
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.