Transcriptional networks in epithelial-mesenchymal transition.

Background: Epithelial-mesenchymal transition (EMT) changes polarized epithelial cells into migratory phenotypes associated with loss of cell-cell adhesion molecules and cytoskeletal rearrangements. This form of plasticity is seen in mesodermal development, fibroblast formation, and cancer metastasis.

Methods And Findings: Here we identify prominent transcriptional networks active during three time points of this transitional process, as epithelial cells become fibroblasts.

CGHsweep: an algorithm for analyzing chromosomal aberrations in genome using aCGH profiles.

DNA copy number aberrations along the genome are vital markers for studying pathogenesis of various diseases including cancers. Array-based Comparative Genome Hybridization (aCGH), which is a high-throughput cytogenetic method, helps in identifying genome-wide copy number aberrations, both gains and losses. Here, we propose a computational technique to analyze aCGH data and to identify potential DNA copy number alterations along the genome.

Constructing human transcriptional regulatory subnets from crossgenome comparison and gene expression profile analysis.

With the completion of Human Genome Project (HGP), understanding the complex interaction between trans- and cis-regulatory elements comprehensively and identifying these potential functional elements are fundamental problems in functional genomics. Although many computational approaches have been developed for lower eukaryotes and prokaryotes, most of them often do not generalize to vertebrates. Here, we use a decay function to characterize transcriptional behavior, and analyze correlations on gene expression profiles of human and mouse to construct coregulated gene groups.