Download Model organism databases and tools

Model Organisms Lab 4-6
18.9.2006 in room MC9 at 13:15-16:00
Petri Pehkonen
Department of Neurobiology
A.I.Virtanen Institute for Molecular Sciences
Model organism databases and tools
The WWW Virtual Library: Model Organisms:
"Many aspects of biology are similar in most or all organisms, but it is frequently much easier to
particular aspects in particular organisms - for instance, genetics is easier in small organisms that
quickly, and very difficult in humans! The most popular model organisms have strong advantag
experimental research, and become even more useful when other scientists have already work
them, discovering techniques, genes and other useful information."
Different information that can be found from model organism databases for a gene include:

Evolutionary information: homologous genes, taxonomic distributions, allele frequencies, syn

Genomic information: chromosomal location, introns, UTRs, regulatory regions, shared dom

Structural information: associated protein structures, fold types, structural domains

Expression information: expression specific to particular tissues, developmental s
phenotypes, diseases

Functional information: enzymatic/molecular function, pathway/cellular role, localization, r
diseases, GO terms

Genetic stocks, vectors, clones

Genetic maps

Large-scale data sets

Genome, EST sets, microarrays, interactions
1
WormBase
Point your browser at the address:
http://wormbase.org
WormBase focusses on model organisms -may have other species, but main part c
only C.Elegans Sequence and other genetic information is primarily sequence oriente
sequence driven.
WormBase site structure:
A. General tools menu
B. Quick search
C. Web site directory including all information in categorized format
A
B
C
C
a) View the release notes. How many genes there are in the database?
b) Look for MAP Kinase Kinase. Search anything with that phrase. You will find CDS
GOs, and Gene Class Summary. Gene Class Summary points to two genes. View
Gene Summary for mek-2, you can see
 [identification] what the gene is
 [location] in the chromosome
 [function] what does it do
 [gene ontology] summary
 [similarities] in other species
 [bibliography] what has been studied
while in Gene Summary View nucleotides (coding/transcript), save the sequence. V
and save also the amino acid sequence. View the function to see if these are
interactions between mek-2 and other genes. Find Gene Ontology terms for this ge
View the similarities in other species. What is the most similar gene? In which spec
Find bibliography, how many citations there is? Click view all to have a look
c) Click the mapping data in the location, you see where is the gene located (Locus
Report): What are the genes nearby? Then use the FIND too to find mek-2 RNAi
Studies (RNAi result), download a early video 1, and terminal video 1. PCR produc
used in the study is sjj_Y54E10B_152.e, download the sequnce.
d) Use the MARKERS tool to find the genomic markers near the location of mek-2
e) Use expression profile tool to retrieve the expression profiles for mek-2. Select the
expression profile Y54E10B_152.C and find the similarly expressed genes within a
radius of 2 units.
f) Use the Batch Genes. Write one term per line: c-fos, mek-1, creb. Click and select
Locus, RNAi, Microarray Probes, NCBI KOGs, Gene ontology terms. Then submit
query.
g) Go to cell reports to find a report for :VB1 Neuron (Cells and Gene Expression C
and Pedigree)
h) Use the saved mek-2 nucleotide sequence to perform a blast.
2
Database handling of model organism data
Microsoft Access database MD.mdb includes 4 tables indicating genes of organisms and
associated transcription factors.
a) Draw ER-model describing the database.
b) Use MS-access to make SQL-query for finding all the genes in Rattus Norvegicus.
c) Make SQL query which associates all genes with associated transcription factors.
d) Use SQL query to find all rat genes and associated transcription factors.
e) Use SQL to count all human genes in database.
f) Use SQL to count all rat transcription factors in database.