ArticleHuman molecular genetics2014
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes.
Article in Human molecular genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 229 papers, 1 of them a synthesis that pooled it.
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Who cites it
229 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Entropy-driven machine learning for deciphering mRNA rearrangement by splicing in complex microorganisms.Frontiers in bioinformatics · 2026Article
- Noncoding RNAs: The Not So "Junk" DNA Is the Blueprint of the Transcriptional Landscape of the RNA World.Experientia supplementum (2012) · 2026Review
- An audit of the PeptideAtlas database uncovers evidence for repurposed pseudogenes and co-opted retroviral ORFs.BMC genomics · 2025Article
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- Predicting the structural impact of human alternative splicing.Genome biology · 2025Article
- A Validated Proteomic Signature of Basal-like Triple-Negative Breast Cancer Subtypes Obtained from Publicly Available Data.Cancers · 2025Article
- The Evolution of Systems Biology and Systems Medicine: From Mechanistic Models to Uncertainty Quantification.Annual review of biomedical engineering · 2025Review
- Three- and four-stranded nucleic acid structures and their ligands.RSC chemical biology · 2025Review
- Embracing Interpersonal Variability of Microbiome in Precision Medicine.Phenomics (Cham, Switzerland) · 2025Article
- The state of the human coding gene catalogues.Database : the journal of biological databases and curation · 2025Article
- A Review of Protein Inference.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Advancements in Single-Cell Proteomics and Mass Spectrometry-Based Techniques for Unmasking Cellular Diversity in Triple Negative Breast Cancer.Proteomics. Clinical applications · 2025Review
169 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
Determining the full complement of protein-coding genes is a key goal of genome annotation. The most powerful approach for confirming protein-coding potential is the detection of cellular protein expression through peptide mass spectrometry (MS) experiments. Here, we mapped peptides detected in seven large-scale proteomics studies to almost 60% of the protein-coding genes in the GENCODE annotation of the human genome. We found a strong relationship between detection in proteomics experiments and both gene family age and cross-species conservation. Most of the genes for which we detected peptides were highly conserved. We found peptides for >96% of genes that evolved before bilateria. At the opposite end of the scale, we identified almost no peptides for genes that have appeared since primates, for genes that did not have any protein-like features or for genes with poor cross-species conservation. These results motivated us to describe a set of 2001 potential non-coding genes based on features such as weak conservation, a lack of protein features, or ambiguous annotations from major databases, all of which correlated with low peptide detection across the seven experiments. We identified peptides for just 3% of these genes. We show that many of these genes behave more like non-coding genes than protein-coding genes and suggest that most are unlikely to code for proteins under normal circumstances. We believe that their inclusion in the human protein-coding gene catalogue should be revised as part of the ongoing human genome annotation effort.
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