Genomics and Bioinformatics Group CIMMiner Genomics and Bioinformatics Group
Examples
Example Heatmap 1
Example Heatmap 2
Example Heatmap 3
Drugs x Cells
Genes x Cells
Genes x Drugs

CIMminer generates color-coded Clustered Image Maps (CIMs) ("heat maps") to represent "high-dimensional" data sets such as gene expression profiles. We introduced CIMs in the mid-1990's for data on drug activity, target expression, gene expression, and proteomic profiles. Clustering of the axes brings like together with like to create patterns of color. (Weinstein, et al., Science 1997; 275:343-349). To learn more details, look at the following articles.

One Matrix CIM
The Clustered Image Map is a 2-dimensional visualization of a real-valued matrix with N rows and M columns (NxM). The CIM has the same number of rows and columns as the matrix and the color at the ith row and jth column is indicative of the corresponding element of the matrix.
Optionally, the rows and/or columns of the matrix can be clustered to identify interesting patterns. This clustering can be done according to several different distance measures and clustering methods.
Two Matrix CIM
Two matrices are used as input in this case, one NxP and another PxM. From these, a third matrix (the product matrix) of size NxM is created where element (i,j) is the correlation between the ith row of the first the jth column of the second matrix. A CIM for the product matrix is created which is colored according to the elements in the various rows and columns.
The rows and/or columns of the product matrix can be clustered to bring out patterns, but here the clustering is done based on the rows of the first input matrix and the columns of the second input matrix. The rows are reordered by clustering the rows of the first input matrix and this reordering is used for the product matrix. Similarly the clustering of the columns of the second input matrix gives the reordering of the columns of the product matrix.

CIMminer is a development of the Genomics and Bioinformatics Group, Developmental Therapeutics Branch (DTB), Developmental Therapeutics Program (DTP), Center for Cancer Research (CCR), National Cancer Institute (NCI). If you have any problems, questions or feedback on the tool, please email us.