Deriving transcriptional programs and functional processes from gene expression databases

Affinity propagation: An exemplar-based tool for clustering in psychological research

Affinity propagation is a message-passing-based clustering procedure that has received widespread attention in domains such as biological science, physics, and computer science. However, its implementation in psychology and related areas of social science is comparatively scant. In this paper, we describe the basic principles of affinity propagation, its relationship to other clustering problems, and the types of data for which it can be used for cluster analysis. More importantly, we identify the strengths and weaknesses of affinity propagation as a clustering tool in general and highlight potential opportunities for its use in psychological research. Numerical examples are provided to illustrate the method.

CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data

Background

Interpreting in vivo sampled microarray data is often complicated by changes in the cell population demographics. To put gene expression into its proper biological context, it is necessary to distinguish differential gene transcription from artificial gene expression induced by changes in the cellular demographics.

Results

CTen (cell type enrichment) is a web-based analytical tool which uses our highly expressed, cell specific (HECS) gene database to identify enriched cell types in heterogeneous microarray data. The web interface is designed for differential expression and gene clustering studies, and the enrichment results are presented as heatmaps or downloadable text files.

Conclusions

In this work, we use an independent, cell-specific gene expression data set to assess CTen's performance in accurately identifying the appropriate cell type and provide insight into the suggested level of enrichment to optimally minimize the number of false discoveries. We show that CTen, when applied to microarray data developed from infected lung tissue, can correctly identify the cell signatures of key lymphocytes in a highly heterogeneous environment and compare its performance to another popular bioinformatics tool. Furthermore, we discuss the strong implications cell type enrichment has in the design of effective microarray workflow strategies and show that, by combining CTen with gene expression clustering, we may be able to determine the relative changes in the number of key cell types.

CTen is available at http://www.influenza-x.org/~jshoemaker/cten/