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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.

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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.

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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!

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OMIM• Search the human genetic diseases which you are interested!• http://www.ncbi.nlm.nih.gov/omim

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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.