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Bioinformatics Assignment
• Project practice:
– We are going to integrate the tools and idea you
learned from this course, and apply them to finish
a project.
– In this project, you have to choose a human gene
which you are interested. Then try to search the
related genes from mouse and zebrafish. Try to dig
out the resources from other animal models to
enhance your understanding of your target gene.
1
Project Practice Report
• The report should contain five parts followed
by the instruction.
• Each part will be count for 20% of your final
score!
• Please hand in you report as a print out hard
copy to Prof. Tzou’s office before Jan 20, 2010.
2
Part 1: Find your target gene
• What kind of human gene are you interested?
– Gene Linked to disease?
• Use OMIM to find your target!
• Paste the OMIM description and translated it to
Chinese in short!
– Other reason
• Please descript it!
3
OMIM
• Search the human genetic diseases which you are interested!
• http://www.ncbi.nlm.nih.gov/omim
4
Example of OMIM search result
Gene Linked to
this disease
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Target Gene Product in FASTA Format
• Select and copy protein sequence!
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Part 2: Protein Domain Analysis
• Use InterProScan to search important domain
of your target protein!
• Please Paste your search result in your report
• Find another tool to do the same work. Also
paste the result in your report.
• Compare the results from the two different
tools.
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InterProScan
• http://www.ebi.ac.uk/InterProScan /
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InterProScan result
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Part 3: Find out ortholog genes in
mouse and zebrafish
• You may use Panther classification system to
find out related genes.
• You may also use BLAST to search for related
genes in mouse or zebrafish.
• Please paste the MGI and Zfin Page of your
target gene in your report.
– Be careful to distinguish between ortholog and
paralog genes
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Panther Tree
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ZFIN gene summary
• http://zfin.org/cgi-bin/webdriver?MIval=aa-ZDB_home.apg
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MGI gene summary
• http://www.informatics.jax.org/
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Part 4: Resources from MGI and Zfin
• Phenotype:
– Knock out phenotype?
– Knock down tool?
– Please include these information in your report!
• Expression Pattern:
–
–
–
–
cDNA, RT-PCR, microarray and in situ hybridization
EST profile in unigene
Please include EST profiles of all ortholog genes.
It is also welcome to put as much as expression
information in your report.
– You may compare the expression profile of ortholog genes
to the human one and discuss about it!
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Linked resource from MGI
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Linked resources from ZFIN
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UniGene
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EST profile
• You have to include
pages of the EST profile
from human, mouse
and zebrafish ortholog
genes!
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Part 5: Open Question of Protein
Analysis
• Please try your best to dig out as many as
possible information to compare the ortholog
genes form mouse and zebrafish by the
internet available tools.
• Hints: protein sorting, translational
modification, 3D structure……etc.
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