Gene Pattern Software from Broad Institute of MIT and Harvard

March 18, 2013

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Research Fellow
BIDMC, Harvard University
Medicine/ Rheumatology
Hierarchical clustering output from Gene Pattern. Gene expression levels of 3 different genes on a total of 96 samples (65 SLE, 27 control and 4 RA) are plotted.

Company:

Broad Institute of MIT and Harvard

Product Name:

Gene Pattern Software

Catalog Number:

N/A
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  • Company: Broad Institute of MIT and Harvard
  • Product Name: Gene Pattern Software
  • Catalog Number: N/A

Over the last couple of years we have been working on potential biomarkers for systemic lupus erythematosus (SLE). We are looking at gene expression levels of a number of genes using real-time PCR in an attempt to see whether these can be used for disease diagnosis or monitoring of disease activity. To investigate the value of a large number of parameters (in our case, gene expression levels) on a large number of samples, novel mathematical techniques like classification trees and hierarchical clustering are needed. These are complicated techniques for the average researcher to learn and the use of graphical user interface software that can assist in these tasks is essential.

GenePattern is online software that provides access to a broad array of computational methods that can be used to analyze large datasets. Compared to other software with similar functionality, it is relatively easy to understand and learn how to use.

Experimental Design and Results Summary

Tips

Most GenePattern modules require cls .gct .res file formatting so once you convert your data into these formats, you are ready to use a large array of different methods in order to analyze them. GenePattern includes modules for a large number of bioinformatics analyses, from allelic discrimination and gene expression to flow cytometry and proteomic studies.

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Hierarchical clustering output from Gene Pattern. Gene expression levels of 3 different genes on a total of 96 samples (65 SLE, 27 control and 4 RA) are plotted.

Summary

The Good

Gene Pattern is probably the best and most comprehensive free online software biomarker discovery and genomic data analysis software packages.

The Bad

Although it is one of the easiest, it may still take some time for the average user to learn how to use. Also, if you plan to work on multiple data analyses, it can be a bit time-consuming.

The Bottom Line

After looking into many free biomarker discovery software packages, this seems to be the easiest to use and the one that offers the greatest array of functions. If you have more time to spend, you may want to try more specialized alternatives, like R and Matlab.

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