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INTRODUCTION TO THE ANTIBODY DATABASE FROM THE
ALLIANCE FOR CELLULAR SIGNALING: TABULATION OF OUR
EXPERIENCE WITH COMMERCIALLY AVAILABLE ANTIBODIES
Heping Han1*, Becky Fulin1, Lonnie Sorrells1, Robert Sinkovits2,
Ruth Levitz1, and Susanne M. Mumby1
The Alliance for Cellular Signaling: The Antibody Laboratory1 (University of
Texas Southwestern Medical Center at Dallas, Dallas TX 75390-9196, USA) and
the Bioinformatics and Data Coordination Laboratory2 (University of California
at San Diego, CA 92037, USA)
INTRODUCTION. The Alliance for Cellular Signaling (AfCS) is a multi-
institutional collaboration with the ultimate goal to mathematically model cellular
signaling (1). Data and protocols from the eight Alliance Laboratories are freely
available on our web site (The AfCS\Nature Signaling Gateway, www.Signaling-
Gateway.org). The intent is for scientists at large to use our data for their own
analysis and to provide leads to follow in their research. The AfCS Antibody
Laboratory has tested numerous commercially available antibodies for their utility
in Western immunoblotting experiments. Antibodies are scored and the tabulated
results posted on the web site in searchable form. The goal for the Antibody
Database is to provide the signaling community with a useful resource that
documents our experience with commercial antibodies.
RESULTS & DISCUSSION. The database currently contains information on
over 300 antibody preparations, most of which are phosphospecific. We have
combined some of the best phosphospecific antibodies for multiplex Western
blotting, which has been employed in ligand screens conducted by the AfCS. The
ligand screen data and the antibody database are located within the Data Center at
www.Signaling-Gateway.org. Under the list of Resources are links to the
database web interface (2) and a report instructing readers on how to navigate the
database and to provide information on how we judge the utility of the antibodies
that we test (3). The web interface is organized into three levels:
1. Index of Antibody Targets, listed alphabetically.
–Click on target name to view next level, the list of antibodies tested against the
chosen target
–Alternatively, the search function at bottom of page may be utilized to find
antibodies of interest by criteria other than the target.
2. List of Antibodies to Chosen Target
–Click on antibody name to view a table that summarizes our Western
immunoblot results for that antibody.
3. Antibody Tables:
–Each row in a table represents results from a separate experiment. Experiments
are scored so that the potential suitability of the test antibodies can be tracked.
We score experiments numerically from 1 to 4 with lower values indicating better
results. The criteria used for scoring phosphospecific antibodies differ from that
of conventional antibodies because of the additional consideration of
phosphosensitivity of the former. Conventional antibodies are scored on two
specific criteria, assigned 1 or 2, while phosphospecific antibodies are scored on
three criteria, assigned 1, 2, or 3 (3). In both cases, a score of 4 is assigned if the
desired criteria are not met.
- Each column of a table is named and numbered. These numbers are linked to
the correct portion of the Explanation of Tables where the reader can find
definitions of column headings.
REFERENCES
1. Participating investigators and scientists of the Alliance for Cellular Signaling
(2002) Nature 420, 703-706
2. Web interface for the AfCS Antibody Database. Access: http://www.signaling-
gateway.org/data/antibody/cgi-bin/targets.cgi
3. Han, H., Sorrells, L., Fulin, B., Levitz, R., Sinkovits, R, Mumby, S.
Introduction to the AfCS Antibody Database: Tabulation of Our Experience with
Commercially Available Antibodies. AfCS Reports [online]. 2003 Vol.1, no.?
[cited October 18, 2004]. Access: http://www.signaling-
gateway.org/reports/v1/DA0007.pdf