ArticleNature communications2016
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 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
46 citing papers in PubMed.
- Review
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- Integrative genomics characterizes HCC eRNAs for prognosis and targeted therapy.Scientific reports · 2025Article
- A large-scale sORF screen identifies putative microproteins involved in cancer cell fitness.iScience · 2025Article
- LncRNA Recognition-Associated CpG Island Detection and Methylation Analysis.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Evidence for widespread translation of 5' untranslated regions.Nucleic acids research · 2024Article
- PCGIMA: developing the web server for human position-defined CpG islands methylation analysis.Frontiers in genetics · 2024Article
- CENTRE: a gradient boosting algorithm for Cell-type-specific ENhancer-Target pREdiction.Bioinformatics (Oxford, England) · 2023Article
- Genome annotation: From human genetics to biodiversity genomics.Cell genomics · 2023Review
- PepQuery2 democratizes public MS proteomics data for rapid peptide searching.Nature communications · 2023Article
- Article
- Improving the genome and proteome annotations of the marine model diatomMarine life science & technology · 2023Article
- Conserved long-range base pairings are associated with pre-mRNA processing of human genes.Nature communications · 2021Article
- Computational Methods for Pseudogene Annotation Based on Sequence Homology.Methods in molecular biology (Clifton, N.J.) · 2021Review
- The Pharmacological Activity of the Wenjing Decoction in Recurrent Spontaneous Abortion.Evidence-based complementary and alternative medicine : eCAM · 2021Article
- Using Deep Learning to Extrapolate Protein Expression Measurements.Proteomics · 2020Article
- An integrative proteogenomics approach reveals peptides encoded by annotated lincRNA in the mouse kidney inner medulla.Physiological genomics · 2020Article
- An analysis of tissue-specific alternative splicing at the protein level.PLoS computational biology · 2020Article
- TENET 2.0: Identification of key transcriptional regulators and enhancers in lung adenocarcinoma.PLoS genetics · 2020Article
- Progress, Challenges, and Surprises in Annotating the Human Genome.Annual review of genomics and human genetics · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Complete annotation of the human genome is indispensable for medical research. The GENCODE consortium strives to provide this, augmenting computational and experimental evidence with manual annotation. The rapidly developing field of proteogenomics provides evidence for the translation of genes into proteins and can be used to discover and refine gene models. However, for both the proteomics and annotation groups, there is a lack of guidelines for integrating this data. Here we report a stringent workflow for the interpretation of proteogenomic data that could be used by the annotation community to interpret novel proteogenomic evidence. Based on reprocessing of three large-scale publicly available human data sets, we show that a conservative approach, using stringent filtering is required to generate valid identifications. Evidence has been found supporting 16 novel protein-coding genes being added to GENCODE. Despite this many peptide identifications in pseudogenes cannot be annotated due to the absence of orthogonal supporting evidence.
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.