Abstract
BackgroundVertebrate genes often appear to cluster within the background of nontranscribed genomic DNA. Here an analysis of the physical distribution of gene structures on human chromosome 7 was performed to confirm the presence of clustering, and to elucidate possible underlying statistical and biological mechanisms.ResultsClustering of genes was confirmed by virtue of a variance of the number of genes per unit physical length that exceeded the respective mean. Further evidence for clustering came from a power function relationship between the variance and mean that possessed an exponent of 1.51. This power function implied that the spatial distribution of genes on chromosome 7 was scale invariant, and that the underlying statistical distribution had a Poisson-gamma (PG) form. A PG distribution for the spatial scattering of genes was validated by stringent comparisons of both the predicted variance to mean power function and its cumulative distribution function to data derived from chromosome 7.ConclusionThe PG distribution was consistent with at least two different biological models: In the microrearrangement model, the number of genes per unit length of chromosome represented the contribution of a random number of smaller chromosomal segments that had originated by random breakage and reconstruction of more primitive chromosomes. Each of these smaller segments would have necessarily contained (on average) a gamma distributed number of genes.In the gene cluster model, genes would be scattered randomly to begin with. Over evolutionary timescales, tandem duplication, mutation, insertion, deletion and rearrangement could act at these gene sites through a stochastic birth death and immigration process to yield a PG distribution.On the basis of the gene position data alone it was not possible to identify the biological model which best explained the observed clustering. However, the underlying PG statistical model implicated neutral evolutionary mechanisms as the basis for this clustering.
Highlights
Vertebrate genes often appear to cluster within the background of nontranscribed genomic DNA
The PG distribution provided an accurate description for the clustering of genes on human chromosome 7
It seemed appropriate to search for a biological mechanism based upon a scale invariant sum of a random (Poisson distributed) number of gamma distributions
Summary
Vertebrate genes often appear to cluster within the background of nontranscribed genomic DNA. An analysis of the physical distribution of gene structures on human chromosome 7 was performed to confirm the presence of clustering, and to elucidate possible underlying statistical and biological mechanisms. The distribution of genes has more to reveal than just this scattering. BMC Evolutionary Biology 2004, 4 http://www.biomedcentral.com/1471-2148/4/3 density of genes within the physical length of human chromosome 7, suggestive of non-random clustering. Syntenic regions within the murine genome exhibited parallel disparities in gene density, a finding that would suggest at least part of this heterogeneity could have originated through evolutionary mechanisms [3]. The object here was to perform such an analysis with the intent to identify statistical and biological mechanisms that might explain the spatial distribution of genes
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