Bioinformatics

Data Analysis Tools

The following resources are available for free use from the Center for Applied Genomics.

 

Event Ratio Program/Directional Change Assessment

The Event Ratio program is a two step program for the analysis of data from Affymetrix GeneChips. This method derives from two observations: 1. Variance is greater for probe sets with low signal intensity; 2. Gene expression is rarely normal. The first part of this tool creates a noise model using a control data set and the second part of the tool selects the probe stets that are the most different directionally between the control and treated samples after filtering out the noise.

Download the Event Ratio Program
Download Documentation

How to reference this tool:

Aris, V.M., Cody, M.J., Cheng, J., Dermody, J.J., Soteropoulos, P., Recce, M. and Tolias, P.P. (2004) Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer. BMC Bioinformatics. 5, 185.

 

E-Z Retrieve

 E-Z Retrieve is a tool for batch retrieval of sequences upstream or downstream from gene origins. This tool enables the search of transcription factor binding sites.

How to reference this tool:

Zhang, H., Ramanathan, Y., Soteropoulos, P., Recce, M., and Tolias, P.P. (2002) EZ-Retrieve: A web-server for batch retrieval of coordinate-specified human DNA sequences and underscoring putative transcription factor-binding sites. Nucleic Acids Research Vol. 30 No. 21 e121

 

WinPrintTip

 WinPrintTip.exe is a short c program that performs the print tip lowess normalization on the result files (gpr files) from Genepix 5.0.

Download WinPrintTip
Download Documentation

Bioinformatics