Genomics/Microarray Facility

Services ( Array Analysis)

Contact: Wen Hwai Horng, M.A.
Tele (215) 898-3902
Fax (215) 898-4521

The array analysis function of the Genomics Facility was established in August 2000. Wen-Hwai Horng will analyze arrays on a fee for array basis. The requests for analysis should be directed to Horng@wistar.org.

This form should be printed out and accompany all Array Images submitted for analysis, providing background information about the RNA quantity, labeling efficiency, and desired comparisons Click here to see a list of the quality measures that we use in considering the useability of hybridized arrays. Certain arrays have a great deal of non-specific hybridization, and appear "dirty", due to inadequate washing or allowing the target to dry out during the hybridization other arrays have a very low signal due to low target specific activity or excess washing. In either case serious consideration should be given to repeating the experiment rather than continuing with the analysis. Click here to view examples of poor arrays.

Phosphoimager files of in-house arrays that are to be analyzed can be either transferred to a file on Casper/MDP or brought to the facility on a Zip disc. The Phosphoimager must be PC controlled, because Mac files are not acceptable to the PC analysis programs. Outside users may use the facility Phosphoimager if necessary and should bring scans to the facility for analysis on a zip disc. A summary of the experiment must be provided, each array clearly identified, and pairwise comparisons that are desired must be listed.

What You Should Expect From The Facility
The array report forms in Microsoft Excel will include the raw data, background values, the normalized data and a report form with gene expression ratios for pairs of arrays if desired. Two types of final reports will be generated: one for Macs, and one for PC. Please state which platform you will need when requesting the analysis.

Special Considerations
In order to access the reports with the database links from a Mac, you will have to download the most recent version of Netscape Navigator (4.7). The Mac reports will have two separate forms, one with links to the Cluster ID and one to the Image Clone ID. The PC version will include direct links to both the Unigene database, via the Cluster ID, and DBest database, via the Image Clone ID. From the gene Cluster site it is possible to connect to several different databases for additional gene information including PubMed. Be sure to drag the report file to your own desktop before trying to open it. It is a large file and will take 10-20 minutes to open over the network, and will take a few minutes to open from your desktop. A facility computer is available for use at a small monthly charge. Questions concerning the reports can be addressed to Michael Showe or Wen Hwai Horng at 215-898-3901 or by email to Showe@wistar.org or Horng@ wistar.upenn.edu.

Facility Software for Expression and Sequence Analysis
In addition to the array analysis software in the facility we also use several programs for sequence alignment, primer design, gene annotation. Wen Hwai is also available to train and assist investigators in the use of facility software to carry out their own analyses and we encourage labs to take advantage of this training. Wistar user groups will be asked to pay a yearly fee of $1,500 which will be charged on a monthly basis of $125 for this service. Complete pricing information, for training and for outside and commercial users is available. This fee will provide access for up to 5 members of a lab to use facility array analysis and DNA sequence analysis programs that are listed below.

Common use software is available for array analysis on facility computers including:

• Imagene: image analysis software
  Imagene, but not other programs, can be installed on investigator's computers under our floating license agreement. Lab must pay one time set-up fee of $100 and monthly $125 fee in order to allow our facility to maintain the most up to date versions of these programs.
  Click here to review our instruction for Imagene
  
  

• ImageQuant (Mac or PC) for visualization of radioactive arrays.

• Atlas Image for Analysis of Clontech Arrays.

• Pathways for analysis of Research Genetics Arrays and

• ArrayVision- Image analysis program that can be used for commercial
  and/or custom arrays, compatible with radioactive or fluorescent
  arrays.

• Sequencher (GeneCodes) - sequence assembly, restriction mapping, Phred and Phrap corrections

• Oligo 5 (NBI) -Primer construction program <

• J-Express: A Java implementation of hierarchical clustering, self organized maps, and principal component analysis.
  
  
• The Stanford Microarray Analysis Suite including:
  
  Cluster performs a variety of types of cluster analysis and other types of processing on large microarray datasets.
  
  TreeView graphically browses results of clustering and other analyses from Cluster. Supports tree-based and image based browsing of hierarchical trees.
  
  
• The Weinstein Laboratory Microarray Analysis Suite
  
  
• Genesight

Database for array data: A MAGEML compliant system based on SQL server is under development.

Useful Online programs

MIA-Molecular Information Agent
The Molecular Information Agent (MIA) searches biological databases to find information about a macromolecule. MIA supports search by molecule identification number, gene symbol, sequence, or keyword.

TIGR - The Institute for Genomic Research
This web site offers free (to not-for-profits) gene analysis software such as Glimmer, a gene locator, and TIGR ArrayViewer for visualizing microarray data (requires purchase of MatLab to access).

Statistical analysis of microarray data

SMD Microarray Links

Classification of Expression Arrays Version CLEAVER 1.0

BRB Array Tools