Signal Transduction Classification Database

This page contains general information on signal transduction classification. It includes links to individual documents, the number of which will increase as more sections of the signal transduction list are revised. This page also provides advice on how to suggest new signal transductions for listing or correction of existing entries.

Motivation

Signal transduction has been of great interest to many academic and pharmaceutical scientists. The regulation of signal transduction is critical for understanding both basic biological processes as well as how they may go awry, leading to disease. With the widespread use of modern biological techniques in various fields of cellular technology, more and more cellular data are accumulated which has led to expansion of knowledge and its terminology. The complexity created by the crosstalk among signal transduction network makes it virtually impossible to infer by hand all the consequences that follow after one modifies one part of the network. Fortunately, a number of databases such as SPAD [Tat95], CSNDB [Tak98] [Tak99], TransPath [Sch01] [Kru03], Sentra [Mal02], GPCR-PD [Hod02], LGICdb [LeN01] and SMART [Let02] have been constructed to bring signal transduction knowledge into a well-organized format, providing simple and fast access to the signal transduction system. The signal molecules and pathways are classified and illustrated by graphs [Bio01]. However, no reference has been made to classification of transductions involving the signal reception, transportation and function. This document presents classifications concerned with signal transductions, and tries to bring order into a nomenclature recommendation of them.

Web version of signal transduction classification

The complete contents of Signal Transduction Classification (Sep 2003) are listed below in order of their signal transduction number, giving just the recommended name. Each entry provides a link to details of that signal transduction. Alternatively if looking for a specific signal transduction, the classification of the broad outline defined by the first two numbers are given below. Each of these subclass entries is linked to a location where the category is divided into sub-subclasses. These, in turn, are linked to a list of recommended names for each signal transduction in the sub-subclass.

List of recommended names for signal transductions

The links are a list of sub-subclasses which in turn list the signal transductions linked to separate files for each signal transduction.

Signal transduction network

Click here to view a signal transduction network (due to the size of the image, please use the left-right scrollbar at the bottom of the page).

Proposed new entries and revised entries

Proposals for new entries to the Signal Transduction List and revisions of previously published entries are available from the following file:

New Signal Transductions

How to suggest new entries and correct existing entries

Information about new signal transductions or corrections to existing entries may be reported directly from these web pages. Advice is available on how to suggest new transductions for listing, or corrections of existing entries. Comments and suggestions on signal transduction classification may be sent to Ming Chen and Susana Lin, Department of Biomedical / Bioinformatics, Technology Institute, Bielefeld University, Germany.

References

[Hod02]  Hodges PE, Carrico PM, Hogan JD, O'Neill KE, Owen JJ, Mangan M, Davis BP, Brooks JE, Garrels JI. (2002) Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics. Nucleic Acids Res. 30(1):137-41

[Kru03]  Krull M,  Voss N, Choi C, Pistor S, Potapov A, Wingender E. (2003) "TRANSPATH®: an integrated database on signal transduction and a tool for array analysis" Nucleic Acids Res. 31(1): 97-100

[LeN01]  Le Novère N and Changeux J-P. (2001) LGICdb: the ligand-gated ion channel database. Nucleic Acids Res. 29(1): 294–295

[Let02]  Letunic I, Goodstadt L, Dickens NJ, Doerks T, Schultz J, Mott R, Ciccarelli F, Copley RR, Ponting CP, Bork P. (2002) Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res. 30(1): 242-244

[Mal02] Malsev N, Marland E, Yu GX, Bhatnagar S, Lusk R. (2002) Sentra, a database of signal transduction proteins. Nucleic Acids Res. 30(1): 349-50

[Sch01] Frank Schacherer, (2001) An object-oriented database for the compilation of signal transduction pathways, dissertation, Von der Gemeinsamen Naturwissenschaftlichen Fakultaet der Technischen Universitaet Carolo-Wilhelmina zu Braunschweig

[Tat95] Naoko Tateishi, Haruki Shiotari, Satoru Kuhara, et al. (1995) An integrated database SPAD (Signaling PAthway Database) for signal transduction and genetic information, Genome Informatics Workshop, GIW95, Dec. 11th-12th Yokohama, Japan

[Tak98] Takai-Igarashi T, Nadaoka Y, Kaminuma T. (1998) A database for cell signaling networks, J Comput Biol 5(4): 747-54

[Tak99] Takai-Igaraschi T, Kaminuma T. (1999) A pathway finding system for the cell signaling networks database. In Silico Biol. 1(3): 129-46

List of signal transduction databases (click here)