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Kyoto Encyclopedia of Genes and Genomes (KEGG)
Biomolecular Reaction pathways for Information Transfer and Expression (BRITE)
Signaling PAthway Database (SPAD)
WIT2 - What Is There
Biocatalysis/Biodegradation Database
Boehringer Mannheim - Biochemical pathways database
ExPASy Biochemical Pathways
Klotho: Biochemical Compounds Declarative Database
GBF - Molecular Bioinformatics of Gene Regulation
TRANSFAC - Transcription Factor database
GeNet - Gene Networks Data Base
GeneNet - Computing System for Automated Gene Network Visualisation
MMP - Main Metabolic Pathways
FlyNets-Interactilist - Direct molecular interactions in Drosophila
Cell Signaling Networks Database
Gene Ontology Consortium
The Biopathways Consortium
National Resource for Cell Analysis and Modelling
E-Cell Project
Kyoto Encyclopedia of Genes and Genomes (KEGG)
This is an attempt to computerize current knowledge of molecular and
cellular biology in terms of the information pathways that consist of
interacting genes and molecules.
KEGG is composed of three interconnected sections: genes, molecules, and pathways, which are also linked to a number of existing databases through our DBGET retrieval system. The genes section contains a functionally classified table of genes for each organism. The classification is based on the pathway section, which contains a number of diagrams representing the flow of information in all known aspects of biological functions. At the moment we are just working on the metabolic pathways. The molecules section also contains classified tables of proteins, RNAs, small molecules, and molecular assemblies.
Biomolecular Reaction pathways for Information Transfer and Expression (BRITE)
This is a graphical database for several species of the biochemical
pathways involved in expression and controlling cell cycles.
Signaling PAthway Database (SPAD)
SPAD is classified into four categories based on extracellular
signal molecule (Growth factor, Cytokine, Hormone and Stress) that
initiate the intracellular signaling pathway. SPAD holds
information on interaction between protein and protein, protein and DNA
as well as the sequence (DNA and protein).
WIT2 - What Is There
The WIT system helps users create metabolic reconstructions, which is
made possible by the recent abundance of complete bacterial genomic
sequences. Such reconstructions will for the first time set the stage
for meaningful simulations of the basic behaviour of microbes, and may
thus significantly advance microbial biology.
The characterization of unicellular life, a scientific endeavor being increasingly driven by large-scale sequencing efforts, is reshaping biology. It is fundamental research that will ultimately be the fountainhead of both insights and applications. The availability of complete genomes is setting the stage for advances and integrations in our understanding of microbial biochemistry and genetics.
Biocatalysis/Biodegradation Database
Microbial biocatalytic reactions and biodegradation pathways primarily
for xenobiotic, chemical compounds.
Boehringer Mannheim - Biochemical pathways database
A search for an enzyme name results in a list of links to the ENZYME Database and, for each entry, links to all maps of"Biochemical
Pathways" in which this entry appears.
ExPASy Biochemical Pathways
This is a searchable database of the Biochemical Pathways" index of
Boehringer Mannheim.
Klotho: Biochemical Compounds Declarative Database
Klotho is part of an attempt to model biological processes, beginning with biochemistry.
GBF - Molecular Bioinformatics of Gene Regulation
The GBF project"Molecular Bioinformatics of Gene Regulation" deals with
the DNA sequence features of regulatory genomic elements and regions, in
particular those that govern transcriptional control. The project
comprises theroretical as well as experimental work. The basis of the
theoretical part is the TRANSFAC database. It compiles data about gene
regulatory DNA sequences and protein factors binding to them. On this
basis, programs are developed that help to identify putative promoter or
enhancer structures and to suggest their features. These efforts are
part of ring funding projects GENUS (GEne regulatory NUcleic acid
Sequences) financed by the BMBF (the previous BMFT) and TRADAT
(TRAnscription DATabases and analysis tools) by the European Comission.
TRANSFAC - Transcription Factor database
TRANSFAC is a database on eukaryotic cis-acting regulatory DNA
elements and trans-acting factors. It covers the whole range from yeast to
human.
The first criterion for a site to be included in TRANSFAC is protein binding, the second is function. Assigned to each site is an unambiguous accession number and an identifier. The latter is composed of a hint onto the species (e. g., HS for human), a code for the gene description and a consecutive number for each entry referring to a particular gene. Thus, HS$BAC_2 refers to the 2nd entry for the human gene for beta-actin.
GeNet - Gene Networks Data Base
The database presents known gene networks organization.
It include maps of gene-gene interactions,
sequences and structure of known regulatory
elements, links to GenBank and Medline references.
GENET is aimed at exploration of areas that are not covered completely by other DBs on gene regulation (EPD, TRRD, COMPEL).
GeneNet - Computing System for Automated Gene Network Visualisation
A program for automated visualization of the gene network based on experimental information presented
in standard format in the GeneNet database.
The regulation of two biological functions antiviral response and hematopoiesis is described in the GeneNet. Gene interdependence, signal transduction pathways and the major features of gene network operation are described for each function. A program provision in Java makes possible automated construction of gene network diagrams.
MMP - Main Metabolic Pathways
A diagram of the main metabolic pathways.
FlyNets-Interactilist - Direct molecular interactions in Drosophila
This contains a preliminary list of molecular interactions occuring in
Drosophila melanogaster. For each one of them, it has been"reasonnably" proven
experimentally (at least one in vivo and one in vitro experiment) that a direct
interaction does indeed occur between two molecular partners.
All interactions described in Interactilist are classified according to their molecular nature which could be either Protein-DNA, Protein-RNA or Protein-protein.
Cell Signaling Networks Database
Cell Signaling Networks Data base (CSNDB) is a data- and knowledge- base
for signaling pathways of human cells. It compiles the information on
biological molecules, sequences, structures, functions, and biological
reactions which transfer the cellular signals. Signaling pathways are
compiled as binary relationships of biomolecules and represented by
graphs drawn automatically.
Gene Ontology Consortium
This is the home of the Gene Ontology Consortium. The goal of the Gene
Ontology Consortium is to produce a dynamic controlled vocabulary that
can be applied to all eukaryotes even as knowledge of gene and protein
roles in cells is accumulating and changing. Although the project's
resources are under development this page is made available now for
community use.
The Biopathways Consortium
Mission
To foster and support the development of technologies and open standards for representing, handling, accessing, analyzing, and adding value to pathways and protein interaction information.
This will be done in an open forum of interested participants through the formation of a consortium of members from different parts of the life science community.
National Resource for Cell Analysis and Modelling
NRCAM provides advanced research tools for the study of cell physiology.
Specifically, computational cell biology is coupled with high resolution
light microscopy to facilitate the interplay between experimental
manipulation and computational simulation of cellular events. The
primary technology development project is the"Virtual Cell", a general
computational framework for modeling cell biological processes. This
new technology associates biochemical and electrophysiological data
describing individual reactions with experimental microscopic image data
describing their subcellular locations. Cell physiological events can
then be simulated within the empirically derived geometries, thus
facilitating the direct comparison of model predictions with experiment.
E-Cell Project
E-CELL, a modeling and simulation environment for biochemical and
genetic processes has been developed. The E-CELL system allows a user
to define functions of proteins, protein-protein interactions,
protein-DNA interactions, regulation of gene expression and other
features of cellular metabolism, as a set of reaction rules. E-CELL
simulates cell behavior by numerically integrating the differential
equations described implicitly in these reaction rules. The user can
observe, through a computer display, dynamic changes in concentrations
of proteins, protein complexes and other chemical compounds in the cell.
Using this software, we constructed a model of a hypothetical cell with
only 127 genes sufficient for transcription, translation, energy
production and phospholipid synthesis. Most of the genes are taken from
Mycoplasma genitalium, the organism having the smallest known
chromosome, whose complete 580kb genome sequence was determined at TIGR
in 1995. We discuss future applications of the E-CELL system with
special respect to genome engineering.under construction
The Glandular Organ Development Database
The Organ Development Database exists to summarise information about gene expre$
phenotypes in a number of developing mammalian glandular organs. Some parts of $
fully functional; others are under construction.
Gene expression in tooth (TOOTHEXP)
Information about expression of different genes in the developing tooth.
The aim is to provide a useful tool for learning and comparing the
expression patterns of different genes and detecting coexpression. For
this purpose a graphical form of presentation is provided where
available.
EpoDB - Erythropoiesis Database
A database of genes that relate to vertebrate red blood cells.
It includes DNA sequence, structural features and potential
transcription factor binding sites.
Prostate Expression Database
This is a public database created by the Molecular Oncology and
Development Team(MOD) at the University of Washington and the CaPCURE
Genetics Consortium. It currently comprises over 50,000 Expressed
Sequence Tags (ESTs) from prostate tissue and cell type-specific cDNA
libraries. The PEDB started as an effort to construct a molecular
fingerprint of the normal, preneoplastic, and neoplastic human prostate.
The database provides:
Any Comments, Questions? Support@hgmp.mrc.ac.uk