Bioinformatics

Microarrays produce large data sets that need to be analyzed and need to be related in many cases to translational and clinical end points. Help with analysis of microarray results are available from the Lineberger Bioinformatics Core and using licensed commercial software for the UNC-CH campus.

For assistance planning microarray experiments and analysis of results:

Contact George Wu at the UNC-CH Lineberger Bioinformatics Core
Phone: 919-843-6669
email: lbg-help@unc.edu to George Wu's attention.

Contact Mike Topal
Phone: 919-966-8208
email: mdtopal@med.unc.edu

Software packages:

GeneSpring and Ingenuity Pathway Assist software packages are both available for use by UNC investigators.

For access to GeneSpring email Hemant Kelkar, Director of the UNC Center for Bioinformatics .

For access to Pathway Assist email Mike Topal

Data Storage:

Shared Drive for Microarray Data Files:

•  The shared drive (\\lbg-netapp1.bioinf.unc.edu) is for storing all microarray files generated by scanning of microarrays (images with tif format) and Feature Extraction Software (converted digital information from images, txt format).

•  The Genomics Core will upload all microarray files to the shared drive (\\lbg-netapp1.bioinf.unc.edu) according to the instructions of shared drive manager in the Bioinformatics Core.

•  Users who want to download their microarray data should apply to the Bioinformatics Core for access to the shared drive.

Data Analysis:

To help analyze your microarray data:

Agilent GeneSpring and Ingenuity Pathways Assist:

UNC provides licenses for these web-based software packages free to UNC investigators, please see information above for access.

UNC Microarray Database (https://genome.unc.edu):

Fill out the "Registration Form" online to get your user name and password emailed to you.
Before contacting the Bioinformatics Core about data analysis, make sure you have successfully uploaded your files into UNC Microarray Database.

•  To upload files to UNC Microarray Database (UMD): After login to the UMD (https://genome.unc.edu/), under “Enter Data”, click  “upload file" to load your file to the UMD.

•  How to match your array data to the correct design-file?

  • From the "Enter Data" page; click "Experiment and Results".
  • Click "Enter a New Experiment into the Database"; choose the correct organism such as Human or Mouse.
  • Choose the scanner used (e.g. choose Agilent if your array was scanned by Agilent Scanner.
  • Select the Print Name: For example, you used an Agilent human 4x44k array with Barcode "251485010727", the 14850 is design  code for this type of array. You should use the print name with 14850 tag.
  • Fill same barcode for all 4 or 8 arrays for each of 4x or 8x slide
  • You have to enter your array files and information one by one. Allow time of your files to upload. You will receive an email to  confirm successful data transfer.
  • After uploading your files, you can view the details by selecting "Advanced Results Search" in the "Search" section. You can display all your data or select data by experiment name, array category and subcategory. Click "display data", you will see the "Search Results" page. Your arrays are listed and you can see raw data, image of arrays, and other files by clicking small icons.

You are now ready to contact the Bioinformatics Core for help to analyze your data.

Call the Genomics Core if you have problems uploading or viewing your files.