Data Sets for Further Analysis

Yeast

• Human Fibroblasts Response to Serum (Stanford University, CA)
• The Transcriptional Program of Sporulation in Budding Yeast (Stanford University, CA)
• Exploring Metabolic and Genetic Control of Gene Expression (Stanford University, CA)
• Array Express Database (by European Bioinformatics Institute, Cambridge, UK)
• TRIPLES: TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces. (Yale University, Connecticut)
  
• Function Junction of the Saccharomyces Genome Database (SGD) Search any yeast gene by name and find out its function. This combines five different databases to give a more integrated view. Very valuable tool. (Stanford University, CA)
• Expression Junction of the Saccharomyces Genome Database (SGD) Type in your favorite gene and discover its expression profile under a wide range of microarray experiments from five different databases. Your gene's expression profile is graphed showing relative expression level vs. time. It is amazing and certainly one of the best genomics teaching sites! Plus.... Your gene is clustered with 20 other genes that exhibit similar profiles. But wait, there's more. For each database's results, you will see two tiny links. One says "web site" and the other says "browse clustered data". Click on "browse clustered data" and you will see the full dataset, and not just a photograph. This is an interactive map that allows you to examine all the genes (~6,200 of them) which have been clustered based on expression profile. This is a treasure trove of information that will keep students and teachers busy mining data that has not been extracted yet. (Stanford University, CA)
• Environmental Stress Response in yeast. This site has 146 different experimental conditions and the microarray analysis for about 6,200 gene for each condition. It is searchable and interactive using the software called Explorer. Very power and rich database. (Stanford University, CA)

Human

E. coli

• ExpressDB RNA Expression Database
  E. coli Data Series: a collection of RNA expression datasets created at the Church Labs and at other laboratories. You can query the database for measures of interest and for selections of ORFs and other features.
• Functional Genomics of E. coli
  characterizing the genome of E. coli by measuring the expression level of every gene under a variety of environmental and genetic conditions. Entire datasets can be downloaded as text files or searched through a database. Additionally, we are working in collaboration with Dr. Julio Collado-Vides lab to develop analysis tools which can be used to map global expression data from E. coli to information such as: operon organization, promoter and regulatory signals upstream of individual genes, and comparisons of the set of affected genes with known and putative transcriptional factors in E.coli.
• Colibri World-Wide Web Server
  This server is constructed around a database dedicated to the analysis of the genome of Escherichia coli: Colibri. Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria.
  Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strainE. coli K-12, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.).
• EcoGene Web Site: EcoWeb
  EcoGene is a collection of information about the genes, proteins, and intergenic regions of the E. coli K-12 genome and proteome accumulated during years of sequence analysis and literature surveys by Kenn Rudd and his collaborators: Mary Berlyn of the E. coli Genetic Stock Center, Amos Bairoch of SWISS-PROT, and Antoine Danchin and Ivan Mozser of Colibri.
• EcoCyc and MetaCyc
  EcoCyc describes all known pathways of E. coli small-molecule metabolism. Each pathway and its component reactions and enzymes are annotated in rich detail, with extensive references to the biomedical literature.
  MetaCyc contains the E. coli pathways of EcoCyc, plus additional pathways that have been gathered from a variety of literature and on-line sources, with citations to the source of each pathway.
  The EcoCyc and MetaCyc databases are accessed through a single WWW server. Users of either database must register for an account.
• The E. coli Index
  These pages contain a comprehensive guide to information relating to the model organism Escherichia coli.
• GenProtEC
  a database dedicated to E. coli genome and proteome. It aims to provide biochemists with the most updated and consolidated information about E. coli genes and proteins resulted from both the traditional experimental reseach and our computational analysis.
• E.coli database collection - ECDC
  In this collection you will find all informatio n regarding the entire E. coli K12 chromosome, we possibly could get. The collection is searchable in different ways. You can go along a gen/sequence map, scroll different tables or just search for a keyword
• Regulon: A DataBase On Transcriptional Regulation in E. Coli
  
• Functional genomics of Escherichia coli in Japan
  Systematic analysis of the shut-off as well as forced expression in vivo of each E. coli ORF and purification of its protein product for further biochemical studies.
  
• Profiling of Escherichia coli chromosome (PEC)
  database has been constructed to compile any relevant information that could help to characterize the E. coli genome, especially with respect to discovering the function of each gene. The database is intended to provide an interface comprehensible to most experimental researchers. TheE. coli genetic resource committee of Japan supports the construction and maintenance of this database.
  

Xenopus

• Xenopus Microarray (Rockefeller University)