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GenePublisher 1.03 Server

-- More than 5000 chips analyzed over the web --

GenePublisher performs automated data analysis from gene expression experiments on a number of different platforms. This server accepts gene tables or Affymetrix CEL files as input, performs numerical and statistical analysis, links the results to various databases, and returns a report of the results. The input data is deleted immediately upon completion of the analysis unless you select the database option below.

If you decide to leave your input data for inclusion in a public database, you get access to a server without input size restrictions.

This is version 1.03 November 22, 2003. Changes since version 1.01:
  • The server now learns from every analysis. It remembers observed associations between genes and uses them to improve the statistical power of future analyses.
  • Your input data can now be stored on the server. Access is controlled by you. The aim is over time to form a large public database of raw microarray data.
If you have any questions or concerns about these changes, please email us.

Sample output report

Input restrictions:

  • The input CEL files must be compressed with gzip (available from and cannot be more than 30 Mbytes in total size. That corresponds to 12 HuGeneFL chips, 10 HG_U95A chips, 22 Focus chips, 8 HG-U133A chips, and so on. The maximum number of chips accepted on this web server is currently 12. There is another server without input restrictions.
  • Avoid using characters _, &, %, # in the input as they may interfere with analysis.

Leave my input data on the server and make it public
(Should you change your mind, just send an email)
Title of report:
Author name, affiliation/email:

Specify CEL files (minimum 4 different files, maximum 12):
File name Category: Name:
File name Category: Name:
File name Category: Name:
File name Category: Name:
File name Category: Name:
File name Category: Name:
File name Category: Name:
File name Category: Name:
File name Category: Name:
File name Category: Name:
File name Category: Name:
File name Category: Name:

OR  specify:

Gene table of raw intensities for each gene in each experiment (minimum 2 replicates of each experiment).
The intensities need to be tab-separated in a text file and use decimal notation (e.g. 712.5). You can have an annotation field in column 2.
This file must not be compressed. Download (shift-click) a sample file of 3 control replicates and 3 experiment replicates from a spotted array of Bacillus subtilis as an example (no header).

File name
Description of file contents (ID=identifier, AN=annotation, A=catgeory A, B=category B, all space separated):

Name experiment columns (space separated):

Is there a header in the first line of the file?

Benjamini-Hochberg correction for multiple testing:
Max number of genes to plot: Max number of false positives:
Select Chip Type
Select Organism
MIAME compliance: In order to comply with the MIAME standard, both for your own report and if you leave the input data on the server for a public database, please add a description of the experimental conditions or give a reference or link to a paper or a manuscript that describes the experiment in detail. The text you write below goes into the materials and methods section of the report you get back (the text is formatted using LaTeX, so you may use LaTeX commands if you like, but avoid using characters _, &, %, #):


Important notes:

  • The analysis can take from 20 minutes to several hours, depending on the number of chips and the statistical analysis performed. The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window.
  • At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.
  • In case of problems with this server, please study any error message carefully, as it will often tell you what the problem is. Look for the first error, as the following errors often are a consequence of the first one. Otherwise, please check the input and make sure that it conforms with the requirements.


For publication of results, please cite:

GenePublisher: Automated Analysis of DNA Microarray Data.
Knudsen, S., Workman, C., Sicheritz-Ponten, T., and Friis, C.
Nucleic Acids Research. Vol. 31, No. 13 3471-3476.


Scientific problems:        Technical problems: