ReviewClinical proteomics2020
Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources.
Review in Clinical proteomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 30 papers.
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
30 citing papers in PubMed.
- Integrated Analysis of Posttranslational Modifications and Total Proteome: Methods for Distinguishing Abundance from Usage Changes.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Pathway and Kinase Analysis in Proteomics and Phosphoproteomics with rROMA.Methods in molecular biology (Clifton, N.J.) · 2027Article
- SCTR-Expressing Astrocyte-Serotonergic Neuron Signaling Drives Sexual Dimorphism in Depression Through KAT7/H4ac-Foxc2 Epigenetic Axis in an AMPK-Dependent Manner.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Integrative Sequencing and Proteogenomic Approaches to Intratumoral Heterogeneity in Cholangiocarcinoma: Implications for Precision Diagnosis and Therapy.Medical sciences (Basel, Switzerland) · 2026Review
- ER-Golgi dysfunction and vesicular transport alterations in rheumatoid arthritis immune cells.Frontiers in immunology · 2026Article
- The hidden Markov model and its applications in bioinformatics analysis.Genes & diseases · 2026Review
- Computational Approaches for Pathway-Centric Analysis of Protein Post-Translational Modifications.Proteomics · 2025Review
- Advanced Proteomics Approaches Hold Potential for the Risk Assessment of Metabolism-Disrupting Chemicals as Omics-Based NAM: A Case Study Using the Phthalate Substitute DINCH.Environmental science & technology · 2025Article
- KINAID: an orthology-based kinase-substrate prediction and analysis tool for phosphoproteomics.Bioinformatics (Oxford, England) · 2025Article
- Yoda1, a Piezo1 agonist, induced latent HIV reactivation associated with upregulation of CD3/TCR complex and HLA genes.Research square · 2025Article
- Advancements in proteogenomics for preclinical targeted cancer therapy research.Biophysics reports · 2025Article
- A web portal for exploring kinase-substrate interactions.NPJ systems biology and applications · 2024Article
- Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.ACS measurement science au · 2024Review
- Calorie restriction and rapamycin distinctly mitigate aging-associated protein phosphorylation changes in mouse muscles.Communications biology · 2024Article
- Bringing CAM photosynthesis to the table: Paving the way for resilient and productive agricultural systems in a changing climate.Plant communications · 2024Review
- Correction to: Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources.Clinical proteomics · 2024Article
- Neuromodulator regulation and emotions: insights from the crosstalk of cell signaling.Frontiers in molecular neuroscience · 2024Review
- Article
- PINK1-PTEN axis promotes metastasis and chemoresistance in ovarian cancer via non-canonical pathway.Journal of experimental & clinical cancer research : CR · 2023Article
- Multi-Omics Integration for the Design of Novel Therapies and the Identification of Novel Biomarkers.Proteomes · 2023Review
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
Mass spectrometry-based phosphoproteomics is becoming an essential methodology for the study of global cellular signaling. Numerous bioinformatics resources are available to facilitate the translation of phosphopeptide identification and quantification results into novel biological and clinical insights, a critical step in phosphoproteomics data analysis. These resources include knowledge bases of kinases and phosphatases, phosphorylation sites, kinase inhibitors, and sequence variants affecting kinase function, and bioinformatics tools that can predict phosphorylation sites in addition to the kinase that phosphorylates them, infer kinase activity, and predict the effect of mutations on kinase signaling. However, these resources exist in silos and it is challenging to select among multiple resources with similar functions. Therefore, we put together a comprehensive collection of resources related to phosphoproteomics data interpretation, compared the use of tools with similar functions, and assessed the usability from the standpoint of typical biologists or clinicians. Overall, tools could be improved by standardization of enzyme names, flexibility of data input and output format, consistent maintenance, and detailed manuals.
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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.