ArticleBioinformatics (Oxford, England)2015
A note on the false discovery rate of novel peptides in proteogenomics.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed.
- Targeting the astrocyte-microglia EFEMP1-GALNT10 axis: a spatially programmable therapeutic strategy for hippocampal vulnerability in Alzheimer's disease.Journal of translational medicine · 2026Article
- Artificial intelligence-, organoid-, and organ-on-chip-powered models to improve pre-clinical animal testing of vaccines and immunotherapeutics: potential, progress, and challenges.Frontiers in artificial intelligence · 2025Review
- Microproteins-Discovery, structure, and function.Proteomics · 2023Review
- Chemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides.Biochemical Society transactions · 2023Review
- Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications inFrontiers in microbiology · 2022Article
- A workflow to identify novel proteins based on the direct mapping of peptide-spectrum-matches to genomic locations.BMC bioinformatics · 2021Article
- GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes.Genome research · 2019Article
- Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.Nature communications · 2018Article
- N-terminal Proteomics Assisted Profiling of the Unexplored Translation Initiation Landscape in Arabidopsis thaliana.Molecular & cellular proteomics : MCP · 2017Article
- GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.Molecular & cellular proteomics : MCP · 2016Article
- Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.Nature communications · 2016Article
- The potential clinical impact of the release of two drafts of the human proteome.Expert review of proteomics · 2015Article
- Harnessing Noncanonical Proteins for Next-Generation Drug Discovery and Diagnosis.WIREs mechanisms of diseaseReview
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.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationProteogenomics has been well accepted as a tool to discover novel genes. In most conventional proteogenomic studies, a global false discovery rate is used to filter out false positives for identifying credible novel peptides. However, it has been found that the actual level of false positives in novel peptides is often out of control and behaves differently for different genomes.
resultsTo quantitatively model this problem, we theoretically analyze the subgroup false discovery rates of annotated and novel peptides. Our analysis shows that the annotation completeness ratio of a genome is the dominant factor influencing the subgroup FDR of novel peptides. Experimental results on two real datasets of Escherichia coli and Mycobacterium tuberculosis support our conjecture. CONTACT: yfu@amss.ac.cn or xupingghy@gmail.com or smhe@ict.ac.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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.