ArticleGenome research2007
Targeted discovery of novel human exons by comparative genomics.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- A genome alignment of 120 mammals highlights ultraconserved element variability and placenta-associated enhancers.GigaScience · 2020Article
- Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants inNPJ genomic medicine · 2019Article
- Intergenically Spliced Chimeric RNAs in Cancer.Trends in cancer · 2016Review
- Long-read sequence assembly of the gorilla genome.Science (New York, N.Y.) · 2016Article
- The Genome 10K Project: a way forward.Annual review of animal biosciences · 2015Review
- Comparative genomic analysis of slc39a12/ZIP12: insight into a zinc transporter required for vertebrate nervous system development.PloS one · 2014Article
- The impact of age, biogenesis, and genomic clustering on Drosophila microRNA evolution.RNA (New York, N.Y.) · 2013Article
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- Predicting site-specific human selective pressure using evolutionary signatures.Bioinformatics (Oxford, England) · 2011Article
- Spectral archives: extending spectral libraries to analyze both identified and unidentified spectra.Nature methods · 2011Article
- Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data.Genome research · 2011Article
- PHAST and RPHAST: phylogenetic analysis with space/time models.Briefings in bioinformatics · 2011Article
- Computational analysis of whole-genome differential allelic expression data in human.PLoS computational biology · 2010Article
- Comparative assessment of methods for aligning multiple genome sequences.Nature biotechnology · 2010Article
- The evolution of epitype.The Plant cell · 2010Article
- Detection of nonneutral substitution rates on mammalian phylogenies.Genome research · 2010Article
- Between a chicken and a grape: estimating the number of human genes.Genome biology · 2010Review
- The completion of the Mammalian Gene Collection (MGC).Genome research · 2009Article
Corrections and comments
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Authors and funding
18 authors.
Funding
Abstract
A complete and accurate set of human protein-coding gene annotations is perhaps the single most important resource for genomic research after the human-genome sequence itself, yet the major gene catalogs remain incomplete and imperfect. Here we describe a genome-wide effort, carried out as part of the Mammalian Gene Collection (MGC) project, to identify human genes not yet in the gene catalogs. Our approach was to produce gene predictions by algorithms that rely on comparative sequence data but do not require direct cDNA evidence, then to test predicted novel genes by RT-PCR. We have identified 734 novel gene fragments (NGFs) containing 2188 exons with, at most, weak prior cDNA support. These NGFs correspond to an estimated 563 distinct genes, of which >160 are completely absent from the major gene catalogs, while hundreds of others represent significant extensions of known genes. The NGFs appear to be predominantly protein-coding genes rather than noncoding RNAs, unlike novel transcribed sequences identified by technologies such as tiling arrays and CAGE. They tend to be expressed at low levels and in a tissue-specific manner, and they are enriched for roles in motor activity, cell adhesion, connective tissue, and central nervous system development. Our results demonstrate that many important genes and gene fragments have been missed by traditional approaches to gene discovery but can be identified by their evolutionary signatures using comparative sequence data. However, they suggest that hundreds-not thousands-of protein-coding genes are completely missing from the current gene catalogs.
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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.