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Assembling a corpus of phosphoproteomic annotations using ProtMapper to normalize site information from databases and text mining

https://doi.org/10.1101/822668
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1016/j.bbamcr.2015.10.008openalex-snapshot
Phosphorylation and isoform use in p120-catenin during development and tumorigenesis
inferredcites →https://doi.org/10.1016/j.cell.2016.05.069openalex-snapshot
Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
inferredcites →https://doi.org/10.1016/j.patter.2021.100257openalex-snapshot
Causal interactions from proteomic profiles: Molecular data meet pathway knowledge
inferredcites →https://doi.org/10.1016/j.semcancer.2019.05.012openalex-snapshot
Role of the PI3K/AKT/mTOR signaling pathway in ovarian cancer: Biological and therapeutic significance
inferredcites →https://doi.org/10.1016/j.tibs.2005.04.013openalex-snapshot
Protein phosphorylation in signaling – 50 years and counting
inferredcites →https://doi.org/10.1016/j.tranon.2018.04.011openalex-snapshot
Combination of PI3K/Akt Pathway Inhibition and Plk1 Depletion Can Enhance Chemosensitivity to Gemcitabine in Pancreatic Carcinoma
inferredcites →https://doi.org/10.1021/acs.biochem.5b00016openalex-snapshot
Plk1 Phosphorylation of IRS2 Prevents Premature Mitotic Exit via AKT Inactivation
inferredcites →https://doi.org/10.1038/nature18003openalex-snapshot
Proteogenomics connects somatic mutations to signalling in breast cancer
inferredcites →https://doi.org/10.1093/database/bay098openalex-snapshot
Large-scale automated machine reading discovers new cancer-driving mechanisms
inferredcites →https://doi.org/10.1093/database/bay128openalex-snapshot
iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature
inferredcites →https://doi.org/10.1093/nar/gkaa980openalex-snapshot
Genenames.org: the HGNC and VGNC resources in 2021
inferredcites →https://doi.org/10.1093/nar/gkj141openalex-snapshot
Human protein reference database--2006 update
inferredcites →https://doi.org/10.1093/nar/gkn653openalex-snapshot
PID: The Pathway Interaction Database
inferredcites →https://doi.org/10.1093/nar/gkr1122openalex-snapshot
PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse
inferredcites →https://doi.org/10.1093/nar/gkv1048openalex-snapshot
SIGNOR: a database of causal relationships between biological entities
inferredcites →https://doi.org/10.1093/nar/gkv1189openalex-snapshot
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
inferredcites →https://doi.org/10.1093/nar/gkx1132openalex-snapshot
The Reactome Pathway Knowledgebase
inferredcites →https://doi.org/10.1093/nar/gky1049openalex-snapshot
UniProt: a worldwide hub of protein knowledge
inferredcites →https://doi.org/10.1109/tcbb.2014.2372765openalex-snapshot
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information
inferredcites →https://doi.org/10.1126/scisignal.aau8645openalex-snapshot
Illuminating the dark phosphoproteome
inferredcites →https://doi.org/10.1158/0008-5472.can-10-1568openalex-snapshot
Upregulation of DLX5 Promotes Ovarian Cancer Cell Proliferation by Enhancing IRS-2-AKT Signaling
inferredcites →https://doi.org/10.1186/1750-2187-5-15openalex-snapshot
AMPK-induced activation of Akt by AICAR is mediated by IGF-1R dependent and independent mechanisms in acute lymphoblastic leukemia
inferredcites →https://doi.org/10.1186/s12859-018-2211-5openalex-snapshot
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining
inferredcites →https://doi.org/10.1371/journal.pbio.0060301openalex-snapshot
Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor
inferredcites →https://doi.org/10.15252/msb.20177651openalex-snapshot
From word models to executable models of signaling networks using automated assembly
inferredcites →https://doi.org/10.15252/msb.202211325openalex-snapshot
Automated assembly of molecular mechanisms at scale from text mining and curated databases
inferredcites →https://doi.org/10.3892/or.2015.3723openalex-snapshot
Misregulation of polo-like protein kinase 1, P53 and P21WAF1 in epithelial ovarian cancer suggests poor prognosis
inferredcites →https://doi.org/10.3892/or.2016.4820openalex-snapshot
Regulation of cell apoptosis and proliferation in pancreatic cancer through PI3K/Akt pathway via Polo-like kinase 1
inferredcites →https://doi.org/10.7717/peerj.11298openalex-snapshot
Measuring pathway database coverage of the phosphoproteome

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1002/1878-0261.13814openalex-snapshot
Molecular and functional profiling unravels targetable vulnerabilities in colorectal cancer
inferred← citeshttps://doi.org/10.1002/1878-0261.70286openalex-snapshot
PAK1 activation drives divergent resistance mechanisms to aromatase inhibition and tamoxifen in a luminal: A breast cancer model
inferred← citeshttps://doi.org/10.1016/j.cell.2020.06.034openalex-snapshot
The Global Phosphorylation Landscape of SARS-CoV-2 Infection
inferred← citeshttps://doi.org/10.1021/acs.jproteome.0c00958openalex-snapshot
PHONEMeS: Efficient Modeling of Signaling Networks Derived from Large-Scale Mass Spectrometry Data
inferred← citeshttps://doi.org/10.1021/acs.jproteome.5c00851openalex-snapshot
Quantitative Tissue Proteomics Reveals Protein Signatures Associated with SARS-CoV-2 Variant Infection in Hamsters
inferred← citeshttps://doi.org/10.1038/s41467-025-59779-yopenalex-snapshot
Comprehensive evaluation of phosphoproteomic-based kinase activity inference
inferred← citeshttps://doi.org/10.1038/s41586-021-04352-yopenalex-snapshot
Evolution of enhanced innate immune evasion by SARS-CoV-2
inferred← citeshttps://doi.org/10.1038/s41589-022-01062-yopenalex-snapshot
Systematic discovery of biomolecular condensate-specific protein phosphorylation
inferred← citeshttps://doi.org/10.1038/s44318-024-00200-7openalex-snapshot
The fitness cost of spurious phosphorylation
inferred← citeshttps://doi.org/10.1093/bib/bbaa390openalex-snapshot
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling
inferred← citeshttps://doi.org/10.1101/2020.04.02.022277openalex-snapshot
A resource for exploring the understudied human kinome for research and therapeutic opportunities
inferred← citeshttps://doi.org/10.1101/2021.06.06.446826openalex-snapshot
Evolution of enhanced innate immune evasion by the SARS-CoV-2 B.1.1.7 UK variant
inferred← citeshttps://doi.org/10.1101/2024.07.23.604744openalex-snapshot
Site-specific metabolic labeling reveals proteome-wide phospho-dynamics
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1010110openalex-snapshot
Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data
inferred← citeshttps://doi.org/10.15252/msb.202110631openalex-snapshot
Pan‐Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival
inferred← citeshttps://doi.org/10.15252/msb.202211325openalex-snapshot
Automated assembly of molecular mechanisms at scale from text mining and curated databases
inferred← citeshttps://doi.org/10.20944/preprints202007.0123.v1openalex-snapshot
The Status of Causality in Biological Databases for Logical Modeling: Data Resources and Data Retrieval Possibilities
inferred← citeshttps://doi.org/10.3389/fcimb.2025.1688880openalex-snapshot
Survival strategies of mycoplasmas: the critical role of post-translational modifications
inferred← citeshttps://doi.org/10.7717/peerj.11298openalex-snapshot
Measuring pathway database coverage of the phosphoproteome
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