Clustering of Gene Expression over Time


Introduction

This web page contains a "K means clustered heat map" summarizing those genes whose expression differed from the healthy control subjects over time. The heat map is identical to the one in the J Exp Med publication (Figure 1) and is interactive. In the 37 healthy control subjects, and 167 severely injured patients, there were 7,028 probe sets representing 5,136 genes whose expression changed with time and were different from controls, using a false discovery rate adjusted probability of p < 0.001 and a 2 fold change. The probe sets have been arranged into 30 clusters or bins based on the similarity of their gene expression pattern. Each row represents a single gene and the expression has been variance normalized: red indicates that the expression is greater than the mean for that gene, white indicates it is equivalent to the mean, and blue indicates that its expression is less than the mean. Each column represents an individual sample from either a control subject or injured patient at the indicated times.

Using this figure, it is possible to examine the patterns of probe sets whose expression are similar, and then to associate them with clinical attributes.

Instructions

By clicking on a cluster on the heat map or the cluster identifier to the left of the heat map, you can view log2 expression scatter plots and box plots of the probe sets in the individual cluster and their associated temporal trajectories, a table of significant gene-sets, a table of associated genes, and a table showing clinical attributes associated with this cluster.








Data and Analysis Description

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