The CDMC has set up two microarray experiment database servers with analysis software that can be used by CDMC customers for a nominal fee ($50 for User account set-up and first year use, and $100 annual renewal fee of account). The software is GeneTraffic® made by Iobion® Informatics.

     GeneTraffic DUO is for two colour spotted arrays like the CDMC arrays.

(Maintenance complete Dec. 17,2009)

     GeneTraffic UNO is for Affymetrix arrays.

The software allows one to upload their microarray experiments into the database and perform numerous types of analyses including: data normalization; comparison of multiple replicates of the same conditions (with statistics); find up- and down-regulated genes; perform gene clustering, etc. The database and analysis software is accessible over the internet using Microsoft Internet Explorer 6 on a PC computer.

For more information about the Genetraffic® software hosted at the CDMC, including tutorials and walkthroughs to help set up and analyze your project, please follow the link to our Genetraffic® information page or contact our This e-mail address is being protected from spam bots, you need JavaScript enabled to view it .

To help users retrieve data from either single genes or lists of genes from our arrays, we have created the following web-accessible databases. These tools are particularly useful for Gene ID conversions.

     14v1 lookup Tool

     12k2 lookup Tool

     12k1 lookup Tool

To rapidly compare Lists of genes we have created a tool examine the intersect, difference and symmetric difference. Please note that this tool automatically removes duplicates

     List Functions Utility
     *temporarily down*

To retrieve GO terms (Gene Ontology, www.geneontology.org) associated with genes or gene lists we have created a tool that links Drosophila CG numbers to GO terms and categorizes the terms based on Biological Process, Molecular Function, Cellular Component. Please note that this tool maintains the order of the input list.

     CDMC GOLookup

We would also like to suggest the following tools to help in the analysis of your array data:

regulatory sequence analysis

'TOUCAN is a workbench for regulatory sequence analysis on metazoan genomes : comparative genomics, detection of significant transcription factor binding sites, and detection of cis-regulatory modules (combinations of binding sites) in sets of coexpressed/coregulated genes.

It is a platform independent, standalone Java application that is tightly linked with Ensembl, and was built using the BioJava package.SOAP web services are used to remotely access multiple algorithms for comparative genomics, motif detection, and module detection.'

     TOUCAN 2      - from Katholieke Universiteit Leuven

Functional Analysis

To examine Gene Lists for over-representations of functional terms based on annotation from Gene Ontology (GO, www.geneontology.org) we have found the following web-based tools highly useful:

     EASE/DAVID      - from NIH, NIAD

     FATIGO      - from Centro de Investigacion Principe Felipe, Valencia, Spain

Classic CDMC datamining tools