BIOL398-01/S11:Week 14

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  Introduce the DNA microarray experiment that was performed.
  Introduce the DNA microarray experiment that was performed.
* States what is unknown about the problem
* States what is unknown about the problem
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  You want to analyze the data with GenMAPP/MAPPFinder, but can't because there is no Gene Database for your species
+
  Little is known about which transcription factors regulate the early response to cold shock
* States clues that suggest how to approach the unknown
* States clues that suggest how to approach the unknown
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  Introduce XMLPipeDB and GenMAPP Builder as the answer to this problem
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  Introduce the workflow of performing statistical analysis of the microarray data, clustering and GO term analysis, and finding candidate transcription factors with YEASTRACT
* States the question the paper is trying to address
* States the question the paper is trying to address
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  In this case you want to discover new information about the microarray data using GenMAPP
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  Using the model to estimate the relative contribution of each transription factor to the regulation of gene expression
=== Methods ===
=== Methods ===
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* This section will summarize the entire workflow for the project.  This needs to be a narrative description of what your team actually did.
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* This section will summarize the entire workflow for the project.  This needs to be a narrative description of what you actually did, but it is not a protocol or recipe. For each step, describe in words what you did and why.
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# Download the UniProt XML proteome set and GOA (GO association) files from [http://www.ebi.ac.uk/integr8/EBI-Integr8-HomePage.do Integr8] for your species.
+
# A description of the experimental design for your assigned microarray dataset
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#* Note the date of download and the version of the file from the [http://www.ebi.ac.uk/integr8/HelpAction.do?action=searchById&refId=5 status page].
+
# The steps you performed in Excel
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# Download GO terms from [http://www.geneontology.org/GO.downloads.ontology.shtml Gene Ontology] in the OBO-XML format, the "obo-xml.gz" file.
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# Using STEM
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# Create the GenMAPP Builder tables in PostgreSQL.
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# Using YEASTRACT
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# Load files into PostgreSQL database via GenMAPP Builder.
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# Using the model
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# Export into a GenMAPP Gene Database.
+
 
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# Inspect/vet/validate Gene Database.
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=== Results & Discussion ===
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# Prepare microarray data (organize, normalize, perform statistical analysis)
+
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# Run GenMAPP using the Gene Database.
+
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#* Microarray data (import using Expression Dataset Manager)
+
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#* Run MAPPFinder analysis
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#* Place genes on MAPP and draw pathway
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=== Results ===
 
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* Gene Database Schema
 
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* Gene Database Testing Report on final version of Gene Database
 
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* Report on quantity and identity of gene IDs that did not make it into the database
 
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*# Gene IDs that were not in the XML source at all
 
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*# Gene IDs that were in the XML source but did not get imported into Postgres
 
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*# Gene IDs that were in Postgres but did not get exported to the GenMAPP Gene Database
 
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* Report on what changes need to be made to the GenMAPP Builder code in order to to accommodate the second and third type of missing gene IDs
 
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** If your team was able to make such changes, report on the results of these changes
 
* Report results of the DNA microarray analysis
* Report results of the DNA microarray analysis
** How many genes were significantly increased and decreased in the dataset? (including your criteria for a significant increase or decrease)
** How many genes were significantly increased and decreased in the dataset? (including your criteria for a significant increase or decrease)
** Table of MAPPFinder results (from .xls)
** Table of MAPPFinder results (from .xls)
** GenMAPP MAPP of a pathway relevant to your results
** GenMAPP MAPP of a pathway relevant to your results
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=== Discussion ===
 
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* How well did the GenMAPP Builder process work for your species (just comment on the technical aspects here, you will discuss the teamwork/process aspects in your individual assessment).
 
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* Discuss the MAPPFinder results for your microarray dataset.  Compare it to what was reported in the original paper you got the microarray data from.
 
=== References ===
=== References ===

Revision as of 10:52, 19 April 2011

BIOL398-01: Biomathematical Modeling

MATH 388-01: Survey of Biomathematics

Loyola Marymount University

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UNDER CONSTRUCTION

This journal entry is due on Tuesday, April 26 at midnight PDT (Monday night/Tuesday morning). NOTE new due date and that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.

Contents

Individual Journal Assignment

  • Store this journal entry as "username Week 14" (i.e., this is the text to place between the square brackets when you link to this page).
  • Create the following set of links. (HINT: you can do all of this easily by adding them to your template and then using the template on your pages.)
    • Link to your journal entry from your user page.
    • Link back from your journal entry to your user page.
    • Link to this assignment from your journal entry.
    • Don't forget to add the "BIOL398-01/S11" category to the end of your wiki page.

Preparation for Final Paper/Presentation

The purpose of this week's assignment is to prepare you for the final paper and presentation due during Finals week.

Final Paper

Style Sheet

Use the following guidelines when formatting your paper.

  • 1" margins
  • double-spaced
  • Times New Roman, 12 point font
  • Number the pages
  • Title page should include a descriptive title for your project, your name, the course number and name, and the date of submission
Introduction

The introduction gives the background information necessary to understand your paper. The introduction should be in the form of a logical argument that "funnels" from broad to narrow:


Shared Journal Assignment

  • Store your journal entry in the shared Class Journal Week 14 page. If this page does not exist yet, go ahead and create it (congratulations on getting in first :) )
  • Link to your journal entry from your user page.
  • Link back from the journal entry to your user page.
  • Sign your portion of the journal with the standard wiki signature shortcut (~~~~).
  • Add the "BIOL398-01/S11" category to the end of the wiki page (if someone has not already done so).

Reflection

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