Phylogenetic modeling of heterogeneous gene-expression microarray data from cancerous specimens.

ABSTRACT: The qualitative dimension of gene expression data and its heterogeneous nature in cancerous specimens can be accounted for by phylogenetic modeling that incorporates the directionality of altered gene expressions, complex patterns of expressions among a group of specimens, and data-based rather than specimen-based gene linkage. Our phylogenetic modeling approach is a double algorithmic technique that includes polarity assessment that brings out the qualitative value of the data, followed by maximum parsimony analysis that is most suitable for the data heterogeneity of cancer gene expression. We demonstrate that polarity assessment of expression values into derived and ancestral states, via outgroup comparison, reduces experimental noise; reveals dichotomously expressed asynchronous genes;

SUBMITTER: Abu-Asab MS 

PROVIDER: S-EPMC2583934 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature