Mapping functional transcription factor networks from gene expression data

A critical step in understanding how a genome functions is determining which transcription factors (TFs) regulate each gene. Accordingly, extensive effort has been devoted to mapping TF networks. In Saccharomyces cerevisiae, protein–DNA interactions have been identified for most TFs by ChIP-chip, and expression profiling has been done on strains deleted for most TFs. These studies revealed that there is little overlap between the genes whose promoters are bound by a TF and those whose expression changes when the TF is deleted, leaving us without a definitive TF network for any eukaryote and without an efficient method for mapping functional TF networks. This paper describes NetProphet, a novel algorithm that improves the efficiency of network mapping from gene expression data. NetProphet exploits a fundamental observation about the nature of TF networks: The response to disrupting or overexpressing a TF is strongest on its direct targets and dissipates rapidly as it propagates through the network. Using S. cerevisiae data, we show that NetProphet can predict thousands of direct, functional regulatory interactions, using only gene expression data. The targets that NetProphet predicts for a TF are at least as likely to have sites matching the TF's binding specificity as the targets implicated by ChIP. Unlike most ChIP targets, the NetProphet targets also show evidence of functional regulation. This suggests a surprising conclusion: The best way to begin mapping direct, functional TF-promoter interactions may not be by measuring binding. We also show that NetProphet yields new insights into the functions of several yeast TFs, including a well-studied TF, Cbf1, and a completely unstudied TF, Eds1

Current Understanding of Circulating Tumor Cells - Potential Value in Malignancies of the Central Nervous System

Detection of circulating tumor cells (CTCs) in the blood via so-called 'liquid biopsies' carries enormous clinical potential in malignancies of the central nervous system (CNS) because of the potential to follow disease evolution with a blood test, without the need for repeat neurosurgical procedures with their inherent risk of patient morbidity. To date studies in non-CNS malignancies, particularly in breast cancer, show increasing reproducibility of detection methods for these rare tumor cells in the circulation. However, no method has yet received full recommendation to use in clinical practice, in part because of lack of a sufficient evidence base regarding clinical utility. In CNS malignancies one of the main challenges is finding a suitable biomarker for identification of these cells, because automated systems such as the widely used Cell Search system are reliant on markers such as the epithelial cell adhesion molecule (EpCAM) which are not present in CNS tumors. This review examines methods for CTC enrichment and detection, and reviews the progress in non-CNS tumors and the potential for using this technique in human brain tumors

Capacitating Community: The Writing Innovation Symposium

The topic of this symposium, capacitating community, invites CLJ readers to consider what makes community possible. This piece showcases one means, small conferences, via a retrospective on the Writing Innovation Symposium (WIS), a regional event with national scope that has hosted writers and writing educators annually in Milwaukee, WI, since 2018. Through a quilted conversation pieced from hours of small-group discussion, twenty-nine participants across academic and nonacademic ranks, roles, and ranges of experience offer insight into the WIS as well as the nature and value of professional community

Capacitating Community: The Writing Innovation Symposium

The topic of this symposium, capacitating community, invites CLJ readers to consider what makes a community possible. This piece showcases one means, small conferences, via a retrospective on the Writing Innovation Symposium (WIS), a regional event with national scope that has hosted writers and writing educators annually in Milwaukee, WI, since 2018. Through a quilted conversation pieced from hours of small-group discussion, twenty-nine participants across academic and nonacademic ranks, roles, and ranges of experience offer insight into the WIS as well as the nature and value of professional community