Educational Sites Related to Genomics and Bioinformatics
Undergraduate Genomics, Proteomics and Bioinformatics Courses
(email your URL and I will add it to the list)
- 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.
3) Cellular Component (where - where is this located e.g. Golgi,
- 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
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,
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
- Link to UCSC Genome Viewer from human CloneReports
- Link to NCBI Genome Viewer from human GeneReports
- Link to EBI's ENSEMBL from human GeneReports
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.
Arrays a high through-put method for screening tissue using your favorite
antibody. (by Dan Pierce, Davidson Colleg '03)
you wanted to know about Microarrays
- Pirelli Award Winning Animation about DNA microarrays
and data analysis
Bacterial Genomes that have been sequenced
- E. coli databases
Eukaryotic Genomes that have been sequenced
Archaea Genomes that have been sequenced
Viral Genomes that have been sequenced
Organelle Genomes (mitochondria and chloroplast) that have been sequenced
- Library of Microarray Publications
(e-library) from TeleChem/arrayit.com
- DNA Microarray
Animation (by A. Malcolm Campbell, Davidson College)
collection of animations from chip production through data analysis
Learning Center (by David Micklos, Cold Spring
Harbor Laboratory, NY)
complete listing of yeast ORFs (UCLA)
helpful listing of all yeast ORFs based on function,
location, EC number, etc.
Easy to browse and search. (MIPS: Munich Information center for Protein
Databases S. cerevisiaeS. pombe
and C. elegans (Merck and Incyte)
- Pat Brown's
Yeast Microarray Page (Stanford University, CA)
Microarray Database (SMD which includes GCAT
Code Yeast Knockout strains
- mini Transposon (mTn)
Yeast Knockout strains (Yale University)
TRansposon-Insertion Phenotypes, Localization,
and Expression in Saccharomyces.
- Institute for
Systems Biology (Seattle, WA)
Cell (freeware for creating computer models of
cells or cellular compartments)
GENE Project (GENE = Genetics Education Networking
and Enhancement; Kansas State Univ., USA)
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
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.
Functional Analysis of the Arabidopsis Genome via Global Gene Expression
Analysis and Gene Disruption
Database (MIPS: Munich Information center for Protein Sequences)
- Links to Genome
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).
Databases S. cerevisiae S. pombe
and C. elegans (by Merck and Incyte)
- Genomics and Bioinformatics
Group at NCI/NIH. (Human) John Weinsteins Laboratory of
Molecular Interaction Maps (Human) Kurt W. Kohn, 1999 Molec.
Biol. Cell 10(8): 2703 - 2734
- Map A: Cyclins & E2F
- Map B: p53 & DNA repair
GCAT Home Page
Biology Home Page
© Copyright 2003 Department of Biology, Davidson College,
Davidson, NC 28035
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