ArticleBioinformatics (Oxford, England)2011
Analyzing marginal cases in differential shotgun proteomics.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- A nitroalkene derivative of salicylate, SANA, induces creatine-dependent thermogenesis and promotes weight loss.Nature metabolism · 2025Trial
- Core-sheath coupling controls flagellar curvature and motility inbioRxiv : the preprint server for biology · 2026Article
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- Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation.Nature microbiology · 2023Article
- Eukaryotic-like gephyrin and cognate membrane receptor coordinate corynebacterial cell division and polar elongation.bioRxiv : the preprint server for biology · 2023Article
- Simple, efficient and thorough shotgun proteomic analysis with PatternLab V.Nature protocols · 2022Review
- Challenges and Opportunities for Bayesian Statistics in Proteomics.Journal of proteome research · 2022Review
- Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism.Infection and immunity · 2021Article
- Proteomics pinpoints alterations in grade I meningiomas of male versus female patients.Scientific reports · 2020Article
- Article
- GeLC-MS-based proteomics of Chromobacterium violaceum: comparison of proteome changes elicited by hydrogen peroxide.Scientific reports · 2016Article
- The influence of iron on the proteomic profile of Chromobacterium violaceum.BMC microbiology · 2014Article
- Article
- Evaluation of normalization methods on GeLC-MS/MS label-free spectral counting data to correct for variation during proteomic workflows.Journal of the American Society for Mass Spectrometry · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
summaryWe present an approach to statistically pinpoint differentially expressed proteins that have quantitation values near the quantitation threshold and are not identified in all replicates (marginal cases). Our method uses a Bayesian strategy to combine parametric statistics with an empirical distribution built from the reproducibility quality of the technical replicates. AVAILABILITY: The software is freely available for academic use at http://pcarvalho.com/patternlab.
Indexed as
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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.