Review For Transpath

Title: TRANSPATH Signal Transduction Browser


Date Reviewed: May 8, 2000

Description: This site is a great place to learn about the signal transduction
             cascades of the cell. One can search the database by entering
             a molecule and the server will return an extensive review of the
             molecule and the pathways it is found in. After entering the molecule
             name, a page is presented which provides a few of the main literature
             references on the molecule and a brief description of the class of
             the molecule, its subtypes, and a few of trhe major upstream and
             downstream partners. Links are provides to all the molecules mentioned
             in relation to yours. One can then build a cascade for the original
             molecule which provides a rather extensive flow chart of the upstream
             and/or downstream partners. At the build a cascade screen, one is given
             many options.  First, one can choose whether to look at upstream or
             downstream partners, or both. Then one can choose how many steps away
             from the opriginal molecule to be shown(0-30). Another niced option is
             to choose a certain type of molecule in the cascade(cytokine, effector,
             transcription factor, etc) and the pathway will be shown with the type
             of molecule chosen highlighted. Finally, one can restrict the flow chart
             which is presented according to species, cells, tissues or compartments.

Strengths: This site can provide an extensive flow chart representing the signaling
           pathways involving a certain molecule. All molecules mentioned are
           hyperlinked to such that the same can be done for those molecules as
           with the original. The homepage also has a category called Modeling
           which provides a brief, yet nice, description of signal transduction
           and many of its terms.

Weaknesses: The site is still under construction, so there may be other problems.
            One problem is that the links to the literature references do not
            work.  The author, title, and pubmed number are available, though, so
            one could look them up themselves.  Another problem is the option to
            restrict the flow chart by species, cells, tissues or compartments when
            building a pathway.  This did not work, but building an unrestricted
            pathway works really well.

Comprehensiveness: Very comprehensive.  Includes many, if not all, of the known
                   upstream and downstream partners, along with a brief description
                   of each molecules role(activation, phosphorylation, inhibition,

Timeliness: This site is pretty good with this respect. In some case a little wait
            may be required, but no more that 1-2 minutes(it is well worth the

Ease of Use: Everything is linked really nicely and the site is very easy to figure

Responsiveness: Very

Similar or Related Sites: The following were provided, with links, on the TRANSPATH
                          homepage(Csndb and BRITE appear to be restricted, though).

Csndb ( strives to be a general database on signal transduction. It uses the same dataset that serves as the base for Transpath and the
Transpath project is conducted in cooperation with Csndb. Csndb has a browse, query and an automated graph image inteface. Csndb is built and curated by Takako
Takai-Igarashi, National Institute of Health Sciences, Japan.

BRITE ( is specializing in cell cycle controlling pathways. It contains data from human, budding yeast and fission
yeast. It contains three hand made clickable maps for the organisms and the possibility to search for a text string. It uses KEGGS dbget
( facility to retrieve information about its pathway components.

Spad ( the moment has hand made, clickable maps for 16 different pathways, grouped by their initializing extracellular messengers.
Some parts of the page are japanese only. Spad is maintained by Professor Satoru Kuhara (Hakozaki Higashi-ku, Fukuoka, 812-8581, Japan Graduate School of Genetic
Resources Technology, Kyushu University), and two assistant Professors.

KEGG ( contains pathways that consist of interacting molecules or genes. It builds upon the DBGET database integration
system, has extensive documentation, manually drawn clickable maps, text search, is fully crosslinked. At the moment is contains a limited, increasing number of
signalling pathways. KEGG is maintained in the Institute for Chemical Research, Kyoto University as part of the Japanese Human Genome Program, under lead of
Minoru Kanehisa. There are about 30 database specialists, programmers and curators.

Overall Evaluation: Excellent