HemI: A Toolkit for Illustrating Heatmaps

Abstract

Recent high-throughput techniques have generated a flood of biological data in all aspects. The transformation and visualization of multi-dimensional and numerical gene or protein expression data in a single heatmap can provide a concise but comprehensive presentation of molecular dynamics under different conditions. In this work, we developed an easy-to-use tool named HemI (Heat map Illustrator), which can visualize either gene or protein expression data in heatmaps. Additionally, the heatmaps can be recolored, rescaled or rotated in a customized manner. In addition, HemI provides multiple clustering strategies for analyzing the data. Publication-quality figures can be exported directly. We propose that HemI can be a useful toolkit for conveniently visualizing and manipulating heatmaps. The stand-alone packages of HemI were implemented in Java and can be accessed at http://hemi.biocuckoo.org/down.php.

Figure 1. Usage of HemI 1.0.

(A) The numerical data in one of three file formats can be directly loaded, whereas the data area can be selected by dragging or holding-SHIFT-then-click manipulations. Titles for X-axis or Y-axis can also be specified; (B) Multiple options for manipulating the heatmp; (C) The numeric data can be clustered for either or both of X-axis and Y-axis; (D) Publication-quality figures can be exported, and two figure formats were supported.

Figure 2. Illustrating heatmaps by HemI 1.0.

(A) Thermal shifts, which indicate binding affinities of 185 compounds to 13 PARPs, were measured by DSF. A higher value represents a stronger binding affinity. (B) Totally, 428 androgen-repressed genes were identified from LNCaP cells, after the treatment of 1 nM synthetic androgen R1881 for 3, 6, 12, 24 and 48 hours. Values shown were normalized to 0 hour and log² transformed.