ArticlePloS one2011
Proteogenomic analysis of bacteria and archaea: a 46 organism case study.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 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
33 citing papers in PubMed.
- Large-scale proteogenomics characterization of microproteins in Mycobacterium tuberculosis.Scientific reports · 2024Article
- Proteogenomic Gene Structure Validation in the Pineapple Genome.Journal of proteome research · 2024Article
- Article
- A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry.Journal of bacteriology · 2022Article
- Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides.microLife · 2022Article
- Are Antisense Proteins in Prokaryotes Functional?Frontiers in molecular biosciences · 2020Article
- InvestigatingMolecular & cellular proteomics : MCP · 2019Article
- Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes.BMC genomics · 2019Article
- In-depth analysis of Bacillus subtilis proteome identifies new ORFs and traces the evolutionary history of modified proteins.Scientific reports · 2018Article
- Modeling leaderless transcription and atypical genes results in more accurate gene prediction in prokaryotes.Genome research · 2018Article
- Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.Genome biology and evolution · 2018Article
- An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics.Genome research · 2017Article
- GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.Molecular & cellular proteomics : MCP · 2016Article
- Unbiased Mitoproteome Analyses Confirm Non-canonical RNA, Expanded Codon Translations.Computational and structural biotechnology journal · 2016Article
- The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity.Scientific data · 2015Article
- Toward a standard in structural genome annotation for prokaryotes.Standards in genomic sciences · 2015Article
- Systems Biology Approaches to Understand Natural Products Biosynthesis.Frontiers in bioengineering and biotechnology · 2015Review
- Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework.Journal of proteome research · 2014Article
- Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data.Proteomics · 2014Article
- Proteogenomics of Gammarus fossarum to document the reproductive system of amphipods.Molecular & cellular proteomics : MCP · 2014Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Experimental evidence is increasingly being used to reassess the quality and accuracy of genome annotation. Proteomics data used for this purpose, called proteogenomics, can alleviate many of the problematic areas of genome annotation, e.g. short protein validation and start site assignment. We performed a proteogenomic analysis of 46 genomes spanning eight bacterial and archaeal phyla across the tree of life. These diverse datasets facilitated the development of a robust approach for proteogenomics that is functional across genomes varying in %GC, gene content, proteomic sampling depth, phylogeny, and genome size. In addition to finding evidence for 682 novel proteins, 1336 new start sites, and numerous dubious genes, we discovered sites of post-translational maturation in the form of proteolytic cleavage of 1175 signal peptides. The number of novel proteins per genome is highly variable (median 7, mean 15, stdev 20). Moreover, comparison of novel genes with the current genes did not reveal any consistent abnormalities. Thus, we conclude that proteogenomics fulfills a yet to be understood deficiency in gene prediction. With the adoption of new sequencing technologies which have higher error rates than Sanger-based methods and the advances in proteomics, proteogenomics may become even more important in the future.
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.