Hierarchical Clustering Explorer (HCE) is a data visualization tool designed for biologists who are trying to understand the functions of genes. To study genes, biologists run experiments using tools called microarrays which measure gene activities under different experimental conditions. Common approaches to finding patterns in the data of these experiments is to run clustering methods but there are few tools that allow for interactive exploration of this data, which can also be quite huge in size. HCE is an example of such a tool that was designed to help in the analysis of clustered datasets.
This image shows three different clusters of genes related to muscle regeneration. These were identified using the tool and in the picture are currently selected for further exploration.
Since HCE was developed for microarray data analysis at the beginning, it is well-known to microarray researchers. There are quite a few biology journal papers that cited HCE as an analysis tool for their microarray data. The most prevalent usage pattern in this field is that users play with features of the system until they see a meaningful separation of clusters. Then they identify clusters that deserve further investigations and look at them in other views of HCE. Once they find such clusters, they often generate a hypothesis that genes in the cluster might have similar or related biological functions to focus/target genes. Using this discovery process, a team of molecular biologists at the Children's Research Institute could identify 18 genes involved in the muscle regeneration process.
Currently, there are many microarray researchers who use HCE as their primary tool for microarray data exploration and a future version has been requested. The good news is that the authors of the tool have recently received funding to develop a newer, and hopefully even better, version of HCE.
Please visit the Discovery Exhibition entry for further information on unexpected impact in teaching and meteorology that the tool has received. If are personally interested in these types of impact stories, please consider submitting to the exhibit. The deadline is now, and please check the call for participation.
This is a guest blog post by Petra Isenberg.