Title: TRANSPATH Signal Transduction Browser
Date Reviewed: May 8, 2000
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.
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.
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.
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,
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
of Use: Everything is linked really nicely
and the site is very easy to figure
or Related Sites: The following were provided,
with links, on the TRANSPATH
homepage(Csndb and BRITE appear to be restricted, though).
( http://geo.nihs.go.jp/csndb.html) 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.
( http://www.genome.ad.jp/brite/CellCycleMaps.html) is specializing in
cell cycle controlling pathways. It contains data from human, budding yeast
yeast. It contains three hand made clickable maps for the organisms and the possibility to search for a text string. It uses KEGGS dbget
(http://www.genome.ad.jp/dbget/dbget.links.html) facility to retrieve information about its pathway components.
( http://www.grt.kyushu-u.ac.jp/spad)at the moment has hand made, clickable
maps for 16 different pathways, grouped by their initializing extracellular
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.
( http://www.genome.ad.jp/kegg/kegg.html) 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