We provide access and expertise in the use of a variety of analysis programs for the analysis of DNA microarray data. These are publicly available programs that are available for download to your own computer. Alternatively, the programs are also available in the computer room of the microarray center (207 Jones).

Duke Integrated Genomics (DIG) Annotation System
A relational database system for storage of a variety of functional information sources linked to the genes included on most microarrays utilized within the Duke Microarray Center.

SAM
This software was developed at Stanford and is known as Significance Analysis of Microarrays. SAM identifies genes with statistically significant changes in expression by assimilating a set of gene specific t tests (for more information about SAM, see http://www-stat.stanford.edu/~tibs/SAM/pnassam.pdf).

• Download the SAM software to your computer.

Cluster
A program developed by Michael Eisen for the analysis of gene expression data using hierarchical clustering, self-organizing maps (SOMs), k-means clustering, and principal component analysis. Hierarchical clustering methods described in Eisen et al. (1998) PNAS 95:14863.

• Download the Cluster software to your computer.

TreeView
A program developed by Michael Eisen for visualization of the results of microarray data analysis. One can graphically browse results of clustering and other analyses from Cluster. Supports tree-based and image based browsing of hierarchical trees. Multiple output formats for generation of images for publications.

• Download the TreeView software to your computer.

dChip
A program developed by Wing Wang's lab at Harvard known as DNA-Chip Analyzer (dChip). dChip is a model-based analysis of oligonucleotide expression arrays that uses a probe-sensitivity index to capture the response characteristic of a specific probe pair and calculates model-based expression indexes. dChip is described in Genome Biol. 2001;2(8):RESEARCH0032 and J Cell Biochem Suppl 2001;Suppl 37:120-5.

• Download the dCHIP software to your computer.

GeneSpring
The Microarray Core Facility has a site license for GeneSpring®. The software allows one to visualize, organize and manipulate gene expression data. GeneSpring 4.2 now offers drag-and-drop file loading and exporting; intensity-dependent normalization that corrects for dye bias in two-color data; a new scatterplot view with enhanced functionality; a display options window to easily control and fine-tune the appearance of your data; and an advanced find genes feature that allows the creation of new gene lists based on annotations. You can download a demo of the software and then contact Holly Dressman (dress002@mc.duke.edu or 668-1583) to obtain the site license password that will enable use of GeneSpring on your computer.

• Download a GeneSpring demo to your computer.

Partek
The Microarray Core Facility has a site license for Partek. Partek Pro features the Analytical SpreadsheetTM and Pattern Visualization SystemTM, that it is a comprehensive data processing, analysis, and visualization system for microarray data. You can download a demo of the software and then contact Holly Dressman (dress002@mc.duke.edu or 668-1583) to obtain the site license password that will enable use of Partek on your computer.

• Download a Partek demo to your computer.

Gene Annotation Tools: Onto-Express (developed at the Department of Computer Science, Wayne State University)
Using strings of accession or cluster identification numbers, Onto-Express searches the public databases and returns tables that correlate expression profiles with the cytogenetics gene locations, the biochemical and molecular functions, the biological processes, cellular components and cellular roles of the translated proteins. The profiles created by Onto-Express fundamentally increase the value of gene expression analyses by facilitating the translation of quantitative value sets to records that contain biological implications.

• Go to Onto-Express

Resourcerer 5.0 (developed at TIGR)
RESOURCERER (Genome Biology 2001 PDF) provides annotation based on the TIGR Gene Indices (TGI) for commomly available microarray resources, including widely used clone sets and Affymetrix GeneChip Arrays. RESOURCERER also allows comparisons between resources from the same species using either TGI or UniGene and between species using the EGO database.

• Go to Resourcerer