Partial correlation analysis indicates causal relationships between GC-content, exon density and recombination rate in the human genome.
BACKGROUND
Several features are known to correlate with the GC-content in the human genome, including recombination rate, gene density and distance to telomere. However, by testing for pairwise correlation only, it is impossible to distinguish direct associations from indirect ones and to distinguish between causes and effects.


RESULTS
We use partial correlations to construct partially directed graphs for the following four variables: GC-content, recombination rate, exon density and distance-to-telomere. Recombination rate and exon density are unconditionally uncorrelated, but become inversely correlated by conditioning on GC-content. This pattern indicates a model where recombination rate and exon density are two independent causes of GC-content variation.


CONCLUSIONS
Causal inference and graphical models are useful methods to understand genome evolution and the mechanisms of isochore evolution in the human genome.
Freudenberg
Jan
J
The Robert S Boas Center for Genomics and Human GeneticsFeinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY 11030, USA. jan.freudenberg@gmail.com
Wang
Mingyi
M
Yang
Yaning
Y
Li
Wentian
W
D001482:Base Composition; D003198:Computer Simulation; D019143:Evolution, Molecular; D005091:Exons; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D011995:Recombination, Genetic / Q000235:genetics*; D016615:Telomere / Q000235:genetics / Q000378:metabolism