ReviewMolecular bioSystems2012
Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis.
Review in Molecular bioSystems, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 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
106 citing papers in PubMed, 1 synthesis or guideline pooled it, 207 citations in OpenAlex.
- A Systematic Review of the Application of Graph Neural Networks to Extract Candidate Genes and Biological Associations.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2025Pooled it
- Integrative Phosphoproteomic Characterization of ULK1 Phosphosites Reveals Co-Regulatory Networks in Autophagy and Metabolic Adaptation.International journal of molecular sciences · 2026Article
- ProteomeScout v4: An open-source, harmonized, ecosystem for post-translational modifications.bioRxiv : the preprint server for biology · 2026Article
- Salmonella SopB suppresses post-transcriptionally regulated cytokine release to reduce early tissue inflammation and delay disease progression.Nature communications · 2026Article
- Exploring the AAK1 Phospho-signaling Landscape Through Phospho-centric Co-regulation Network.Cell biochemistry and biophysics · 2026Article
- Exploring the Phosphoregulatory Network of Human Sucrose Non-Fermenting 1-Related Kinase.Biology · 2026Article
- Cell type-specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease.Genome research · 2026Article
- Illuminating the Co-Phosphoregulatory Network of the Dark Kinase STK10 by Omics Approaches.BioMed research international · 2026Article
- EPSD 2.0: An Updated Database of Protein Phosphorylation Sites Across Eukaryotic Species.Genomics, proteomics & bioinformatics · 2025Article
- Unravelling the human taste receptor interactome: machine learning and molecular modelling insights into protein-protein interactions.NPJ science of food · 2025Article
- PKA-Mediated Phosphorylation of SFRP4 Promotes Wnt/β-Catenin Activation and Cancer Stemness in Gastric Cancer.International journal of molecular sciences · 2025Article
- Identification of Parkinson's disease PACE subtypes and repurposing treatments through integrative analyses of multimodal data.NPJ digital medicine · 2024Article
- GPS-SUMO 2.0: an updated online service for the prediction of SUMOylation sites and SUMO-interacting motifs.Nucleic acids research · 2024Article
- Predicting gene disease associations with knowledge graph embeddings for diseases with curtailed information.NAR genomics and bioinformatics · 2024Article
- Geometric graph neural networks on multi-omics data to predict cancer survival outcomes.Computers in biology and medicine · 2023Article
- Splicing Modulators Are Involved in Human Polyglutamine Diversification via Protein Complexes Shuttling between Nucleus and Cytoplasm.International journal of molecular sciences · 2023Article
- Multi-omics analysis reveals distinct non-reversion mechanisms of PARPi resistance in BRCA1- versus BRCA2-deficient mammary tumors.Cell reports · 2023Article
- Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data.Cell reports methods · 2023Article
- AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations.Nucleic acids research · 2023Article
- Proteomic-Based Discovery of Predictive Biomarkers for Drug Therapy Response and Personalized Medicine in Chronic Immune Thrombocytopenia.BioMed research international · 2023Article
46 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 at 4 institutions in 2 countries.
Funding
Abstract
Human Protein Reference Database (HPRD) is a rich resource of experimentally proven features of human proteins. Protein information in HPRD includes protein-protein interactions, post-translational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization of human proteins. Although, protein-protein interaction data from HPRD has been widely used by the scientific community, its phosphoproteome data has not been exploited to its full potential. HPRD is one of the largest documentations of human phosphoproteins in the public domain. Currently, phosphorylation data in HPRD comprises of 95,016 phosphosites mapped on to 13,041 proteins. Additionally, enzyme-substrate reactions responsible for 5930 phosphorylation events were also documented. Significant improvements in technologies and high-throughput platforms in biomedical investigations led to an exponential increase of biological data and phosphoproteomic data in recent years. Human Proteinpedia, a community annotation portal developed by us, has also contributed to the significant increase in phosphoproteomic data in HPRD. A large number of phosphorylation events have been mapped on to reference sequences available in HPRD and Human Proteinpedia along with associated protein features. This will provide a platform for systems biology approaches to determine the role of protein phosphorylation in protein function, cell signaling, biological processes and their implication in human diseases. This review aims to provide a composite view of phosphoproteomic data pertaining to human proteins in HPRD and Human Proteinpedia.
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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.