Welcome to the GenomeWeb
Regulation & Cellular-Level Databases

Search for:

This is a collection of genome databases that give information on the regulation and interaction of genes and gene products and their functioning up to the level of cells and beyond.

[info] Kyoto Encyclopedia of Genes and Genomes (KEGG)
[info] Biomolecular Reaction pathways for Information Transfer and Expression (BRITE)
[info] Signaling PAthway Database (SPAD)
[info] WIT2 - What Is There
[info] Biocatalysis/Biodegradation Database
[info] Boehringer Mannheim - Biochemical pathways database
[info] ExPASy Biochemical Pathways
[info] Klotho: Biochemical Compounds Declarative Database
[info] GBF - Molecular Bioinformatics of Gene Regulation
[info] TRANSFAC - Transcription Factor database
[info] GeNet - Gene Networks Data Base
[info] GeneNet - Computing System for Automated Gene Network Visualisation
[info] MMP - Main Metabolic Pathways
[info] FlyNets-Interactilist - Direct molecular interactions in Drosophila
[info] Cell Signaling Networks Database
[info] Gene Ontology Consortium
[info] The Biopathways Consortium
[info] National Resource for Cell Analysis and Modelling
[info] E-Cell Project

Embryology, Organ development and Body Plan Databases

[info] The Glandular Organ Development Database
[info] Gene expression in tooth (TOOTHEXP)
[info] EpoDB - Erythropoiesis Database
[info] Prostate Expression Database

Detailed information on the above options

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

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