Skip Navigation

Nucleic Acids Research 2006 34(Database Issue):D546-D551; doi:10.1093/nar/gkj107
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (909K) Freely available
Right arrow Screen PDF (301K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Krull, M.
Right arrow Articles by Wingender, E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Krull, M.
Right arrow Articles by Wingender, E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2006, Vol. 34, Database issue D546-D551
© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

TRANSPATH®: an information resource for storing and visualizing signaling pathways and their pathological aberrations

Mathias Krull1,*, Susanne Pistor1, Nico Voss1, Alexander Kel1, Ingmar Reuter1, Deborah Kronenberg2, Holger Michael2, Knut Schwarzer2, Anatolij Potapov1,2, Claudia Choi1, Olga Kel-Margoulis1 and Edgar Wingender1,2

1BIOBASE GmbH Halchtersche Strasse 33, D-38304 Wolfenbüttel, Germany 2Department of Bioinformatics, Medical School, University of Göttingen Goldschmidtstrasse 1, D-37077 Göttingen, Germany

*To whom correspondence should be addressed. Tel: +49 5331 8584 32; Fax: +49 5331 8584 70; Email: mathias.krull{at}biobase-international.com

Received September 15, 2005. Revised October 17, 2005. Accepted October 17, 2005.

TRANSPATH® is a database about signal transduction events. It provides information about signaling molecules, their reactions and the pathways these reactions constitute. The representation of signaling molecules is organized in a number of orthogonal hierarchies reflecting the classification of the molecules, their species-specific or generic features, and their post-translational modifications. Reactions are similarly hierarchically organized in a three-layer architecture, differentiating between reactions that are evidenced by individual publications, generalizations of these reactions to construct species-independent ‘reference pathways’ and the ‘semantic projections’ of these pathways. A number of search and browse options allow easy access to the database contents, which can be visualized with the tool PathwayBuilderTM. The module PathoSign adds data about pathologically relevant mutations in signaling components, including their genotypes and phenotypes. TRANSPATH® and PathoSign can be used as encyclopaedia, in the educational process, for vizualization and modeling of signal transduction networks and for the analysis of gene expression data. TRANSPATH® Public 6.0 is freely accessible for users from non-profit organizations under http://www.gene-regulation.com/pub/databases.html.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
A. Keller, C. Backes, A. Gerasch, M. Kaufmann, O. Kohlbacher, E. Meese, and H.-P. Lenhof
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis
Bioinformatics, November 1, 2009; 25(21): 2787 - 2794.
[Abstract] [Full Text] [PDF]

Home page
 J R Soc InterfaceHome page
J. P. Goncalves, M. Graos, and A. X.C.N. Valente
POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data
J R Soc Interface, October 6, 2009; 6(39): 881 - 896.
[Abstract] [Full Text] [PDF]

Home page
 Mol. Cell. ProteomicsHome page
S. Stahl, E. Fung, C. Adams, J. Lengqvist, B. Mork, B. Stenerlow, R. Lewensohn, J. Lehtio, R. Zubarev, and K. Viktorsson
Proteomics and Pathway Analysis Identifies JNK Signaling as Critical for High Linear Energy Transfer Radiation-induced Apoptosis in Non-small Lung Cancer Cells
Mol. Cell. Proteomics, May 1, 2009; 8(5): 1117 - 1129.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
H. Michael, J. Hogan, A. Kel, O. Kel-Margoulis, F. Schacherer, N. Voss, and E. Wingender
Building a knowledge base for systems pathology
Brief Bioinform, December 10, 2008; (2008) bbn038v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
Y. Li, P. Hao, S. Zheng, K. Tu, H. Fan, R. Zhu, G. Ding, C. Dong, C. Wang, X. Li, et al.
Gene expression module-based chemical function similarity search
Nucleic Acids Res., November 1, 2008; 36(20): e137 - e137.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
G. Sanguinetti, J. Noirel, and P. C. Wright
MMG: a probabilistic tool to identify submodules of metabolic pathways
Bioinformatics, April 15, 2008; 24(8): 1078 - 1084.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Donitz, B. Goemann, M. Lize, H. Michael, N. Sasse, E. Wingender, and A. P. Potapov
EndoNet: an information resource about regulatory networks of cell-to-cell communication
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D689 - D694.
[Abstract] [Full Text] [PDF]

Home page
 Cancer Res.Home page
B. Kim, H. J. Lee, H. Y. Choi, Y. Shin, S. Nam, G. Seo, D.-S. Son, J. Jo, J. Kim, J. Lee, et al.
Clinical Validity of the Lung Cancer Biomarkers Identified by Bioinformatics Analysis of Public Expression Data
Cancer Res., August 1, 2007; 67(15): 7431 - 7438.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Backes, A. Keller, J. Kuentzer, B. Kneissl, N. Comtesse, Y. A. Elnakady, R. Muller, E. Meese, and H.-P. Lenhof
GeneTrail--advanced gene set enrichment analysis
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W186 - W192.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. Degenhardt, M. Haubrock, J. Donitz, E. Wingender, and T. Crass
DEEP--A tool for differential expression effector prediction
Nucleic Acids Res., July 13, 2007; 35(suppl_2): W619 - W624.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
H. C. Mak, M. Daly, B. Gruebel, and T. Ideker
CellCircuits: a database of protein network models
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D538 - D545.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.