Hierarchical clustering with multiple-height branch-cut applied to short time-series gene expression data.

Rigid adherence to pre-specified thresholds and static graphical representations can lead to incorrect decisions on merging of clusters. As an alternative to existing automated or semi-automated methods, we developed a visual analytics approach for performing hierarchical clustering analysis of short time-series gene expression data. Dynamic sliders control parameters such as the similarity threshold at which clusters are merged and the level of relative intra-cluster distinctiveness, which can be used to identify "weak-edges" within clusters. An expert user can drill down to further explore the dendrogram and detect nested clusters and outliers. This is done by using the sliders and by pointing and clicking on the representation to cut the branches of the tree in multiple-heights. A prototype of this tool has been developed in collaboration with a small group of biologists for analysing their own datasets. Initial feedback on the tool has been positive.

MLCut: exploring multi-level cuts in dendrograms for biological data.

Choosing a single similarity threshold for cutting dendrograms is not sufficient for performing hierarchical clustering analysis of heterogeneous data sets. In addition, alternative automated or semi-automated methods that cut dendrograms in multiple levels make assumptions about the data in hand. In an attempt to help the user to find patterns in the data and resolve ambiguities in cluster assignments, we developed MLCut: a tool that provides visual support for exploring dendrograms of heterogeneous data sets in different levels of detail. The interactive exploration of the dendrogram is coordinated with a representation of the original data, shown as parallel coordinates. The tool supports three analysis steps. Firstly, a single-height similarity threshold can be applied using a dynamic slider to identify the main clusters. Secondly, a distinctiveness threshold can be applied using a second dynamic slider to identify “weak-edges” that indicate heterogeneity within clusters. Thirdly, the user can drill-down to further explore the dendrogram structure - always in relation to the original data - and cut the branches of the tree at multiple levels. Interactive drill-down is supported using mouse events such as hovering, pointing and clicking on elements of the dendrogram. Two prototypes of this tool have been developed in collaboration with a group of biologists for analysing their own data sets. We found that enabling the users to cut the tree at multiple levels, while viewing the effect in the original data, is a promising method for clustering which could lead to scientific discoveries.