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 stored on the server to
become part of a public microarray database.
This is the unlimited version without input restrictions. Fixed error in input fields January 13, 2004.
This is version 1.03 January 13, 2004. 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 are now by default stored on the server. Access is controlled by you.
The aim is over time to form a large public database of raw microarray data.
The input CEL files must be compressed with gzip (available from
www.gzip.org).
Avoid using characters _, &, %, # in the input as they may interfere with
analysis.
Specify CEL files (minimum 4 different files): File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory:Name:
File nameCategory: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 2 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. Otherwise,
please check the input and make sure that it conforms with the
requirements.
