ArticleNucleic acids research2013
DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 114 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
114 citing papers in PubMed.
- Multimodal single-cell omics analysis identifies epithelium-immune cell interactions and immune vulnerability associated with sex differences in COVID-19.Signal transduction and targeted therapy · 2021Trial
- CLASPP: A unified model for predicting post-translational modifications.PLoS computational biology · 2026Article
- CLASPP: A unified model for predicting post-translational modifications.bioRxiv : the preprint server for biology · 2026Article
- CysDBase: a comprehensive database of cysteine post-translational modifications across protein sequence, structure, microenvironment, class, cellular localization, biological pathway, and taxonomy.Database : the journal of biological databases and curation · 2026Article
- Precision Profiling of the Cardiovascular Post-Translationally Modified Proteome.Journal of cardiovascular development and disease · 2026Review
- Article
- DCPPS: Prediction of Kinase-Specific Phosphorylation Sites Using Dynamic Embedding and Cross-Representation Interaction.Interdisciplinary sciences, computational life sciences · 2025Article
- Genome-scale exon perturbation screens uncover exons critical for cell fitness.Molecular cell · 2024Article
- Identification of Parkinson's disease PACE subtypes and repurposing treatments through integrative analyses of multimodal data.NPJ digital medicine · 2024Article
- Global-Scale Profiling of Differential Expressed Lysine-Lactylated Proteins in the Cerebral Endothelium of Cerebral Ischemia-Reperfusion Injury Rats.Cellular and molecular neurobiology · 2023Article
- Applications of deep learning in understanding gene regulation.Cell reports methods · 2023Review
- Interpretable deep learning translation of GWAS and multi-omics findings to identify pathobiology and drug repurposing in Alzheimer's disease.Cell reports · 2022Article
- NESM: a network embedding method for tumor stratification by integrating multi-omics data.G3 (Bethesda, Md.) · 2022Article
- KSTAR: An algorithm to predict patient-specific kinase activities from phosphoproteomic data.Nature communications · 2022Article
- A comprehensive SARS-CoV-2-human protein-protein interactome network identifies pathobiology and host-targeting therapies for COVID-19.Research square · 2022Article
- Construction and validation of a two-gene signature based on SUMOylation regulatory genes in non-small cell lung cancer patients.BMC cancer · 2022Article
- dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications.Nucleic acids research · 2022Article
- A global map of associations between types of protein posttranslational modifications and human genetic diseases.iScience · 2021Article
- Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment.Alzheimer's research & therapy · 2021Article
- A network-based deep learning methodology for stratification of tumor mutations.Bioinformatics (Oxford, England) · 2021Article
54 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
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.
Indexed as
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.