Isochores merit the prefix 'iso'.
The isochore concept in the human genome sequence was challenged in an analysis by the International Human Genome Sequencing Consortium (IHGSC). We argue here that a statement in the IHGSC's analysis concerning the existence of isochores is misleading, because the homogeneity was not examined at a large enough length scale and consequently an inappropriate statistical test was applied. A test of the existence of isochores should be equivalent to a test of homogeneity or equality of windowed GC%. The statistical test applied in the IHGSC's analysis, the binomial test, is a test of whether individual bases are independent and identically-distributed (iid). For testing the existence of isochores, or homogeneity in windowed GC%, we propose to use another statistical test: the analysis of variance (ANOVA). It can be shown that DNA sequences that are rejected by the binomial test may not be rejected by the ANOVA test.
Li
Wentian
W
Center for Genomics and Human Genetics, North Shore LIJ Research Institute, 350 Community Drive, Manhasset, NY 11030, USA. wli@nslij-genetics.org
Bernaola-Galván
Pedro
P
Carpena
Pedro
P
Oliver
Jose L
JL
D000704:Analysis of Variance; D001482:Base Composition; D016010:Binomial Distribution; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D018899:CpG Islands; D020862:GC Rich Sequence; D015894:Genome, Human; D006801:Humans; D032085:Isochores / Q000737:chemistry*; D015233:Models, Statistical; D017422:Sequence Analysis, DNA / Q000706:statistics & numerical data
D032085:Isochores