Synthetic genetic interactions reveal buffering mechanisms in the cell against genetic perturbations. These interactions have been widely used by researchers to predict functional similarity of gene pairs. In this paper, we perform a comprehensive evaluation of various methods for predicting co-pathway membership of genes based on their neighborhood similarity in the genetic network. We clearly...

In recent years, several pathway analyses of genome-wide association studies reported the involvement of metabolic and immune pathways in Alzheimer's disease (AD). Until now, the exact mechanisms of these pathways in AD are still unclear. Here, we conducted a pathway analysis of a whole genome AD case-control expression dataset (n=41, 25 AD cases and 16 controls) from the human temporal cortex ...

MOTIVATION Based on a gene classification into hierarchical categories ('BINs'), MapMan was originally developed to display Arabidopsis thaliana gene expression in a functional context. We have created a bioinformatics system to extend MapMan to any organism by using a new BIN structure based on the KEGG database. Gene sequences are assigned to this ontology by homology relationships in four re...

Metabolic pathways are composed of a series of chemical reactions occurring within a cell. In each pathway, enzymes catalyze the conversion of substrates into structurally similar products. Thus, structural similarity provides a potential means for mapping newly identified biochemical compounds to known metabolic pathways. In this paper, we present TrackSM, a cheminformatics tool designed to as...

The pathogenesis of Alzheimer's disease is complex. The amyloid hypothesis has directed research efforts for many years, but it has recently been questioned after failed drug trials. Here, we review the evidence for and against and suggest that it might be premature to abandon the amyloid hypothesis.

The impact of environmental and behavioral factors on the 24-h profile of blood pressure (BP) has been well established. Various attempts have been made to control these exogenous factors, in order to investigate a possible endogenous circadian variation of BP. Recently, we reported the results of the first environmentally and behaviorally controlled laboratory study with 24-h recordings of BP ...

Long non-coding RNAs (lncRNAs) have been demonstrated to be significant in numerous biological processes. Hypertension is a form of cardiovascular disease with at least one billion cases worldwide. The present study sought to compare the differential expression profiles of lncRNAs in the renal cortex of spontaneously hypertensive rats (SHRs) and normotensive Wistar‑Kyoto (WKY) rats. The ipsilat...

High-throughput experimental technologies often identify dozens to hundreds of genes related to, or changed in, a biological or pathological process. From these genes one wants to identify biological pathways that may be involved and diseases that may be implicated. Here, we report a web server, KOBAS 2.0, which annotates an input set of genes with putative pathways and disease relationships ba...