ArticleGenome biology2003
Computational comparison of two mouse draft genomes and the human golden path.
Article in Genome biology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers, 1 of them a synthesis that pooled it.
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Who cites it
9 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Retinome - defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium.BMC genomics · 2004Pooled it
- Rat mir-155 generated from the lncRNA Bic is 'hidden' in the alternate genomic assembly and reveals the existence of novel mammalian miRNAs and clusters.RNA (New York, N.Y.) · 2013Article
- Specificity protein-1 as a critical regulator of human cystathionine gamma-lyase in smooth muscle cells.The Journal of biological chemistry · 2011Article
- A comprehensive description of the transcriptome of the hypothalamoneurohypophyseal system in euhydrated and dehydrated rats.Proceedings of the National Academy of Sciences of the United States of America · 2006Article
- What can we learn from noncoding regions of similarity between genomes?BMC bioinformatics · 2004Article
- Neuregulin induces the expression of transcription factors and myosin heavy chains typical of muscle spindles in cultured human muscle.Proceedings of the National Academy of Sciences of the United States of America · 2004Article
- Charting gene regulatory networks: strategies, challenges and perspectives.The Biochemical journal · 2004Review
- The truth about mouse, human, worms and yeast.Human genomics · 2004Article
- The independence of our genome assemblies.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe availability of both mouse and human draft genomes has marked the beginning of a new era of comparative mammalian genomics. The two available mouse genome assemblies, from the public mouse genome sequencing consortium and Celera Genomics, were obtained using different clone libraries and different assembly methods.
resultsWe present here a critical comparison of the two latest mouse genome assemblies. The utility of the combined genomes is further demonstrated by comparing them with the human 'golden path' and through a subsequent analysis of a resulting conserved sequence element (CSE) database, which allows us to identify over 6,000 potential novel genes and to derive independent estimates of the number of human protein-coding genes.
conclusionThe Celera and public mouse assemblies differ in about 10% of the mouse genome. Each assembly has advantages over the other: Celera has higher accuracy in base-pairs and overall higher coverage of the genome; the public assembly, however, has higher sequence quality in some newly finished bacterial artificial chromosome clone (BAC) regions and the data are freely accessible. Perhaps most important, by combining both assemblies, we can get a better annotation of the human genome; in particular, we can obtain the most complete set of CSEs, one third of which are related to known genes and some others are related to other functional genomic regions. More than half the CSEs are of unknown function. From the CSEs, we estimate the total number of human protein-coding genes to be about 40,000. This searchable publicly available online CSEdb will expedite new discoveries through comparative genomics.
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