HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics

Background  

Accurate interpretation of data obtained by unsupervised analysis of large scale expression profiling studies is currently frequently performed by visually combining sample-gene heatmaps and sample characteristics. This method is not optimal for comparing individual samples or groups of samples. Here, we describe an approach to visually integrate the results of unsupervised and supervised cluster analysis using a correlation plot and additional sample metadata.     

Fine filaments in lymphatic endothelial cells

Several and various types of cells contain fine cytoplasmic filaments closely resembling the myofilaments of muscle cells (2, 18, 23, 24). In many of these cells and especially when cultured, it has been demonstrated that some of these filaments react with heavy meromyosin (HMM) in the same way as do the actin filaments of muscle cells (3, 6 7). This suggests that these filaments may be actinoid and form part of a contractile system. As fine intracytoplasmic filaments do occur in lymphatic endothelial cells (2, 14), we undertook an electron microscope investigation of their fine structure and their reaction on incubation with HMM and EDTA. We postulated that lymphatic endothelial cells possess a contractile filamentous system to which these filaments belong.     

Transport and metabolism of carnitine precursors in various organs of the rat

Isolated, vascularly perfused small intestine, liver, and kidney were used to investigate their interdependence in the absorption and metabolism of carnitine precursors in the rat. During 30 min of recirculating perfusion, the small intestine absorbed trimethyllysine, hydroxytrimethyllysine, and trimethylaminobutyrate fairly well when they were administered via the lumen or the perfusate. Trimethylaminobutyrate was synthesized from either trimethyllysine or hydroxytrimethyllysine by the small intestine, but further hydroxylation of trimethylaminobutyrate to carnitine did not occur. Trimethyllysine and hydroxytrimethyllysine were not readily absorbed by the liver. In contrast, trimethylaminobutyrate and trimethylaminobutyraldehyde were rapidly absorbed from the perfusate and readily incorporated into carnitine by the liver. Trimethyllysine and hydroxytrimethyllysine were taken up slowly by the kiodney and partially converted to trimethylaminobutyrate during 3409 min of perfusion. Trimethylaminobutyrate was neither absorbed readily by the kidney nor was it hydroxylated to carnitine. These results were compared to whole animal studies performed over an equivalent time period. The data suggest that the isolted small intestine absorbs trimethyllysine well, but it probably plays a minor role in metabolizing physiological quantities of this compound in the whole animal where other organs are competing for the same substrate. In both the isolated organ and in the whole animal, the kidney absorbs and metabolizes trimethyllysine more readily than the liver; whereas the liver absorbs trimethylaminobutyrate more rapidly than either the kidney or the small intestine and, unlike these organs, converts it to carnitine.