ArticleProteomics2018
Darkness in the Human Gene and Protein Function Space: Widely Modest or Absent Illumination by the Life Science Literature and the Trend for Fewer Protein Function Discoveries Since 2000.
Article in Proteomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 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
26 citing papers in PubMed, 68 citations in OpenAlex.
- A sequence-based classifier distinguishes phenotype-associated genes from other gene models in plants.Genome research · 2026Article
- Proteomic Profiling of GLP-1-Mediated Cardioprotection in a Large Animal Model of Chronic Coronary Artery Disease.Medical research archives · 2025Article
- Overcoming research bias: The untapped potential of biomedically important but understudied proteins.iScience · 2025Article
- Perturbomics: CRISPR-Cas screening-based functional genomics approach for drug target discovery.Experimental & molecular medicine · 2025Review
- A longitudinal analysis of function annotations of the human proteome reveals consistently high biases.Database : the journal of biological databases and curation · 2025Article
- PRESCOTT: a population aware, epistatic, and structural model accurately predicts missense effects.Genome biology · 2025Article
- EvoWeaver: large-scale prediction of gene functional associations from coevolutionary signals.Nature communications · 2025Article
- Learning maximally spanning representations improves protein function annotation.bioRxiv : the preprint server for biology · 2025Article
- Uncharacterized yeast geneeLife · 2024Article
- Review
- Article
- Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system.Nature immunology · 2024Review
- Meta-Research: understudied genes are lost in a leaky pipeline between genome-wide assays and reporting of results.bioRxiv : the preprint server for biology · 2024Article
- Evaluation of input data modality choices on functional gene embeddings.NAR genomics and bioinformatics · 2023Article
- Broad functional profiling of fission yeast proteins using phenomics and machine learning.eLife · 2023Article
- Did the early full genome sequencing of yeast boost gene function discovery?Biology direct · 2023Article
- Functional unknomics: Systematic screening of conserved genes of unknown function.PLoS biology · 2023Article
- Uncharacterized protein C17orf80 - a novel interactor of human mitochondrial nucleoids.Journal of cell science · 2023Article
- About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature.Biology direct · 2023Article
- Protection of the human gene research literature from contract cheating organizations known as research paper mills.Nucleic acids research · 2022Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
The mentioning of gene names in the body of the scientific literature 1901-2017 and their fractional counting is used as a proxy to assess the level of biological function discovery. A literature score of one has been defined as full publication equivalent (FPE), the amount of literature necessary to achieve one publication solely dedicated to a gene. It has been found that less than 5000 human genes have each at least 100 FPEs in the available literature corpus. This group of elite genes (4817 protein-coding genes, 119 non-coding RNAs) attracts the overwhelming majority of the scientific literature about genes. Yet, thousands of proteins have never been mentioned at all, ≈2000 further proteins have not even one FPE of literature and, for ≈4600 additional proteins, the FPE count is below 10. The protein function discovery rate measured as numbers of proteins first mentioned or crossing a threshold of accumulated FPEs in a given year has grown until 2000 but is in decline thereafter. This drop is partially offset by function discoveries for non-coding RNAs. The full human genome sequencing does not boost the function discovery rate. Since 2000, the fastest growing group in the literature is that with at least 500 FPEs per gene.
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.