What is the Marker tool?

The Marker Tool is a bioinformatics tool written in R to predict marker genes from microarray gene expression data sets. The tool expects normalized data and the use of replicates for each sample type. Marker genes are identified by the existence of groupings of samples of the same type with similar expression of the marker gene.

Download: Bioconductor

Score

The score is used to rank the markers according to their specificity. The score values range from 0 to 1. Values near 0 would indicate high specificity and large values closer to 1 would indicate low specificity.

Data Sets

Data Set 1

Microarray gene expression data set derived from five tissue (i.e., lung, liver, heart atrium, kidney cortex, and midbrain) from GEO Serie GSE3526. Each tissue type is represented by three replicates. The data set consists of the following samples:

Data Set 2

Microarray expression data set derived from five tissue (i.e., lung, liver, heart, kidney, and brain) from two GEO Series GSE1133 and GSE2361. Each tissue is represented by three replicates. The data set consists of the following samples:

Data Set 3

Microarray gene expression data set derived from four tissue (i.e., lung, liver, heart, and kidney) from the GEO DataSet GDS596. Each tissue is represented by two replicates. The data set consists of the following samples:

Gene Level

If this option is selected, scoring methods from the tool Jetset (Qiyuan et al.) will be used to select the optimal probe set for each gene and create a simple one-to-one mapping between gene and probe set.