Genome Consortium for Active Teaching

Genomic Sites

Laura Hoopes (Pomona College) tours the labs of Pat Brown (Stanford) and Leroy Hood (Institute for Systems Biology, Seattle).
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. This is the group that has proposed to drop the term "function" and describe three aspects of a proteins role in cells -
1) Biological Process (why - why is this being done? e.g. movement of cell)
2) Molecular Function (what - what kind of molecule is this? e.g. ATPase)
3) Cellular Component (where - where is this located e.g. Golgi, ribosome, etc.)
Participating Groups:
- Drosophila (fruitfly) - FlyBase
- Saccharomyces (budding yeast) - Saccharomyces Genome Database (SGD)
- Mus (mouse) - Mouse Genome Database (MGD) & Gene Expression Database (GXD)
- Arabidopsis (brassica or mustard family) - The Arabidopsis Information Resource (TAIR)
- Caenorhabditis (nematode) - WormBase
MedMiner will extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query. This tool combines the GeneCards and PubMed search engines with user input and automated server-side scripts in an integrated text filtering system. "MedMiner: an Internet Text-Mining Tool for Biomedical Information, with Application to Gene Expression Profiling," L. Tanabe, U. Scherf, L. H. Smith, J. K. Lee, L. Hunter and J. N. Weinstein, BioTechniques 27:1210-1217.
The Stanford Online Universal Resource for Clones and ESTs (SOURCE) compiles information from several publicly accessible databases, including UniGene , dbEST , SwissProt , GeneMap99 , RHdb , GeneCards and LocusLink. The mission of SOURCE is to provide a unique scientific resource that pools publicly available data commonly sought after for any clone, GenBank accession number, or gene. SOURCE was specifically designed to facilitate analysis of the large data sets that biologists can now produce using genome-scale experimental approaches. Five Most Recent Additions:
- Representative sequences on GeneReports
- Search SOURCE using GenBank Accession No. for known genes
- Link to UCSC Genome Viewer from human CloneReports
- Link to NCBI Genome Viewer from human GeneReports
- Link to EBI's ENSEMBL from human GeneReports
GeneCards is a database of human genes, their products and their involvement in diseases. It offers concise information about the functions of all human genes that have an approved symbol, as well as selected others.
Primer for Microarrays (10 MB PDF file) - written by Ramsi Haddad, Ph.D., Research Scientist, Van Andel Research Institute, Grand Rapids, MI.
Tissue Arrays a high through-put method for screening tissue using your favorite antibody. (by Dan Pierce, Davidson Colleg '03)
Everything you wanted to know about Microarrays
Pirelli Award Winning Animation about DNA microarrays and data analysis
All Bacterial Genomes that have been sequenced
E. coli databases for searching
All Eukaryotic Genomes that have been sequenced
All Archaea Genomes that have been sequenced
All Viral Genomes that have been sequenced
All Organelle Genomes (mitochondria and chloroplast) that have been sequenced
Library of Microarray Publications (e-library) from TeleChem/arrayit.com

Yeast

DNA Microarray Animation (by A. Malcolm Campbell, Davidson College)
Excellent collection of animations from chip production through data analysis
DNA Learning Center (by David Micklos, Cold Spring Harbor Laboratory, NY)
A complete listing of yeast ORFs (UCLA)
Very helpful listing of all yeast ORFs based on function, location, EC number, etc.
Easy to browse and search. (MIPS: Munich Information center for Protein Sequences)
Proteome Databases S. cerevisiaeS. pombe and C. elegans (Merck and Incyte)
Pat Brown's Yeast Microarray Page (Stanford University, CA)
Stanford Microarray Database (SMD which includes GCAT student data)
Bar Code Yeast Knockout strains
mini Transposon (mTn) Yeast Knockout strains (Yale University)
TRIPLES: TRansposon-Insertion Phenotypes, Localization, and Expression in Saccharomyces.
Institute for Systems Biology (Seattle, WA)
Virtual Cell (freeware for creating computer models of cells or cellular compartments)
Yeast GENE Project (GENE = Genetics Education Networking and Enhancement; Kansas State Univ., USA)
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. Comparison with C. elegans is included. Very valuable tool.
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.
Arabidopsis
A Functional Analysis of the Arabidopsis Genome via Global Gene Expression Analysis and Gene Disruption
Arabidopsis Database (MIPS: Munich Information center for Protein Sequences)
Other Species
Links to Genome Pages
Leptin Specific Patterns of Gene Expression in White Adipose Tissue (mouse)
Alexander Soukas, Paul Cohen, Nicholas D. Socci, and Jeffrey M. Friedman (Genes and Development 2000. 14: 963).
Proteome Databases S. cerevisiae S. pombe and C. elegans (by Merck and Incyte)
Genomics and Bioinformatics Group at NCI/NIH. (Human) John Weinstein’s Laboratory of Molecular Pharmacology
Kohn Molecular Interaction Maps (Human) Kurt W. Kohn, 1999 Molec. Biol. Cell 10(8): 2703 - 2734
- Map A: Cyclins & E2F
- Map B: p53 & DNA repair

Bioinformatic Sites

Computational Biology (by Laurie Heyer, Davidson College) - Be sure to view project 2 about clutstering. This is an interactive site that helps students understand how hierarchical clustering is done. Project 1 exhibits four live Kyte-Doolittle hydropathy pages.
Integrating Bioinformatics with Labs in Several Undergraduate Courses (by Jeff Newman, Lycoming College, PA)
Darwing 2000 (Very Good Bioinformatics site by Rick Hershberger, Carlow College, PA)
Honors Thesis Creates New Software by Rahul Karnik, class of 2000 Davidson College
C. elegans bioinformatics software and course materials by Betsey Dyer (biology) and Mark LeBlanc (computer science) at Wheaton College, MA
GridIt Resources for Microarrays Including software links for analysis
Proteome Databases S. cerevisiaeS. pombe and C. elegans (Merck and Incyte)

Journals

PubMed (free search of all biomedical journals)
PubCrawler (free automated literature search with email summaries sent to you daily, or weekly, etc.)
BioMed Central (Online journals, completely free)
Genomics Bibliography (Dec. 2000)
The journal Genome Research
The journal Functional & Intergrative Genomics

Companies Listings

Companies that Make Microarrayers and DNA Chips

Educational Sites Related to Genomics and Bioinformatics