ArticleScientific reports2015
Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 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
36 citing papers in PubMed, 63 citations in OpenAlex.
- Multiomics analysis reveals dermokine as a regulator of keratinocyte differentiation and adhesion.JCI insight · 2026Article
- Blood feeding triggers the terminal differentiation of precursor cells in tick salivary glands.Science advances · 2026Article
- Integrative phosphoproteomics reveals kinase-mediated regulation of OCIAD1 and its roles in mitochondrial quality control.Frontiers in bioinformatics · 2026Article
- Blood-Based miRNA Panels for Timely Detection of Non-Small-Cell Lung Cancer: From Biomarker Discovery to Clinical Translation.International journal of molecular sciences · 2025Review
- KRAS-mediated upregulation of CIP2A promotes suppression of PP2A-B56α to initiate pancreatic cancer development.Oncogene · 2024Article
- KRAS-mediated upregulation of CIP2A promotes suppression of PP2A-B56α to initiate pancreatic cancer development.bioRxiv : the preprint server for biology · 2024Article
- Phosphoproteomic investigation of targets of protein phosphatases in EGFR signaling.Scientific reports · 2024Article
- A pyridinium-based strategy for lysine-selective protein modification and chemoproteomic profiling in live cells.Chemical science · 2024Article
- Human pancreatic cancer patients with Epithelial-to-Mesenchymal Transition and an aggressive phenotype show a disturbed balance in Protein Phosphatase Type 2A expression and functionality.Journal of translational medicine · 2023Article
- RAS and PP2A activities converge on epigenetic gene regulation.Life science alliance · 2023Article
- DeepFLR facilitates false localization rate control in phosphoproteomics.Nature communications · 2023Article
- Preventing Respiratory Viral Diseases with Antimicrobial Peptide Master Regulators in the Lung Airway Habitat.Clinics and practice · 2023Review
- Statistical Analysis of Post-Translational Modifications Quantified by Label-Free Proteomics Across Multiple Biological Conditions with R: Illustration from SARS-CoV-2 Infected Cells.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Identifying cytokine signaling signatures in primary human Th-1 cells by phospho-proteomics analysis.STAR protocols · 2021Article
- An integrative multi-omics approach uncovers the regulatory role of CDK7 and CDK4 in autophagy activation induced by silica nanoparticles.Autophagy · 2021Article
- MHC Phosphopeptides: Promising Targets for Immunotherapy of Cancer and Other Chronic Diseases.Molecular & cellular proteomics : MCP · 2021Review
- Systems pharmacology in combination with proteomics reveals underlying mechanisms of Xihuang pill against triple-negative breast cancer.Bioengineered · 2020Article
- PIM1 accelerates prostate cancer cell motility by phosphorylating actin capping proteins.Cell communication and signaling : CCS · 2020Article
- Integrated omics in Drosophila uncover a circadian kinome.Nature communications · 2020Article
- Phosphoproteome and drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1.The Journal of biological chemistry · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Hyperactivated RAS drives progression of many human malignancies. However, oncogenic activity of RAS is dependent on simultaneous inactivation of protein phosphatase 2A (PP2A) activity. Although PP2A is known to regulate some of the RAS effector pathways, it has not been systematically assessed how these proteins functionally interact. Here we have analyzed phosphoproteomes regulated by either RAS or PP2A, by phosphopeptide enrichment followed by mass-spectrometry-based label-free quantification. To allow data normalization in situations where depletion of RAS or PP2A inhibitor CIP2A causes a large uni-directional change in the phosphopeptide abundance, we developed a novel normalization strategy, named pairwise normalization. This normalization is based on adjusting phosphopeptide abundances measured before and after the enrichment. The superior performance of the pairwise normalization was verified by various independent methods. Additionally, we demonstrate how the selected normalization method influences the downstream analyses and interpretation of pathway activities. Consequently, bioinformatics analysis of RAS and CIP2A regulated phosphoproteomes revealed a significant overlap in their functional pathways. This is most likely biologically meaningful as we observed a synergistic survival effect between CIP2A and RAS expression as well as KRAS activating mutations in TCGA pan-cancer data set, and synergistic relationship between CIP2A and KRAS depletion in colony growth assays.
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.