Custom Arrays

ScanArray

The software used to scan your custom/slide-based arrays is called ScanArray. This application allows one to setup a protocol for scanning your resulting microarray slides in a uniform defined manner utilizing the Perkin Elmer ScanArray scanner. In a common two dye approach (Cy3 and Cy5), one first scans with the required parameters for one dye (your experimental) and then does a second scan (your control or reference) set up to capture the scan results from the second dye used.

QuantArray

Once you have created your scanned files for your array using ScanArray software, the next step is to quantify the contribution of signals from each of the given fluorescent dyes associated with each unique spot printed on the slide. QuantArray software is the application utilized for such purposes. This application will generate a text file summary of the determined intensity/expression values for each of the defined printed spots on the slide. 

Cyber-T

Following any necessary adjustments of your collected data results (baseline/background corrections, normalizations, etc.), Cyber-T may be used to statistically determine what genes are truly differentially expressed. Cyber-T is a web-based program, written at UC Irvine, that employs statistical analyses based on simple t- tests that use the observed variance of replicate gene measurements across replicate experiments, or regularized t-tests that use a Bayesian estimate of the variance among gene measurements within an experiment.

GeneSpring GX 

GeneSpring GX (Agilent Technologies) is a commercial software application that displays expression data in ways that help you conceptualize the information in your data. This feature rich software product is available for users at the Facility on a fee for usage basis. First time users of this software are encouraged to download a free trial version of the software from Agilent Technologies to their own computer once they have all of their data ready for analysis. This way they can practice and begin to learn the basics of this full-featured software application prior to starting with the Facility’s copy, which is accessed on a fee for usage basis.

PathwayArchitect

PathwayArchitect (Stratagene) is a commercial software package, which allows users to build Biological Interaction Networks (BINs) based upon your list of genes/proteins of interest from your microarray experimental data. This software allows users to addresses the question, "what molecules are connected to the biological objects in my list?" in order to tease out the relevant pathway or interaction relationships found within your data. Use of the Facility’s copy of this software application is accessed on a fee for usage basis.