BIOL368/F14:Week 15: Difference between revisions
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'''''NOTE that this assignment is UNDER CONSTRUCTION.''''' | '''''NOTE that this assignment is UNDER CONSTRUCTION.''''' | ||
__NOTOC__ | __NOTOC__ | ||
<div style="float: right;">__TOC__</div> | <div style="float: right;">__TOC__</div> | ||
== Background == | |||
=== References === | |||
* Brown, P.O. & Botstein, D. (1999) [http://www.nature.com/ng/journal/v21/n1s/full/ng0199supp_33.html Exploring the new world of the genome with DNA microarrays] ''Nature Genetics'' 21: 33-37. | |||
* Campbell, A.M. and Heyer, L.J. (2003), “Chapter 4: Basic Research with DNA Microarrays”, in ''Discovering Genomics, Proteomics, and Bioinformatics'', Cold Spring Harbor Laboratory Press, pp. 107-124. ([https://mylmuconnect.lmu.edu/webapps/portal/frameset.jsp?tab_tab_group_id=_2_1&url=%2Fwebapps%2Fblackboard%2Fexecute%2Flauncher%3Ftype%3DCourse%26id%3D_33586_1%26url%3D Available on MyLMUConnect]) | |||
* Dahlquist, K.D., Salomonis, N., Vranizan, K., Lawlor, S.C., & Conklin, B.R. (2002) [http://www.nature.com/ng/journal/v31/n1/full/ng0502-19.html GenMAPP, A New Tool for Viewing and Analyzing Microarray Data on Biological Pathways.] Nature Genetics 31: 19-20. | |||
* DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997) [http://www.sciencemag.org/content/278/5338/680.full Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale.] ''Science'' 278: 680-686. | |||
* [http://genomebiology.com/2003/4/1/R7 Doniger et al. (2003)] | |||
* [http://www.biomedcentral.com/1471-2105/8/217 Salomonis et al. (2007)] | |||
=== Overview of DNA Microarray Analysis === | |||
This is a list of steps required to analyze DNA microarray data. | |||
# Quantitate the fluorescence signal in each spot in the microarray image. | |||
#* Typically performed by the scanner software, although third party software packages do exist. | |||
#* The image of the microarray slide and this quantitation are considered the "raw-est" form of the data. | |||
#* Ideally, this type of raw data would be made publicly available upon publication. | |||
#* In practice, the image data is usually not made available because the raw image file of one slide could be up to 100 MB in size. | |||
#* Also, some journals do not require data deposition as a requirement for publication, so often published data are not actually available anywhere for download. | |||
#* Microarray data is not centrally located on the web. Some major sources are: | |||
#** [http://www.ncbi.nlm.nih.gov/geo/ NCBI GEO] | |||
#** [http://www.ebi.ac.uk/microarray-as/ae/ EBI ArrayExpress] | |||
#** [http://smd.stanford.edu/ Stanford Microarray Database] | |||
#** [http://puma.princeton.edu/ PUMAdb (Princeton Microarray Database)] | |||
#** In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site. | |||
# Calculate the ratio of red/green fluorescence | |||
# Log(base 2) transform the ratios | |||
# Normalize the log ratios on each microarray slide | |||
# Normalize the log ratios for a set of slides in an experiment | |||
# Perform statistical analysis on the log ratios | |||
# Compare individual genes with known data | |||
# Look for patterns (expression profiles; clusters) in the data (many programs are available to do this) | |||
# Perform Gene Ontology term enrichment analysis (we will use MAPPFinder for this) | |||
# Map onto biological pathways (we will use GenMAPP for this) | |||
== Individual Journal Assignment == | |||
* Store this journal entry as "''username'' Week 15" (i.e., this is the text to place between the square brackets when you link to this page). | |||
* Create the following set of links. '''''These links should all be in your personal template; then use the template on your journal entry.''''' | |||
** 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 "BIOL368/F14" category to the end of your wiki page. | |||
=== Complete Microarray Data Analysis === | |||
* Using the spreadsheet that you submitted for the [[BIOL368/F14:Week 12 | Week 13 Assignment]], you will now complete GenMAPP and MAPPFinder analysis of your dataset. | |||
** [[BIOL367/F10:GenMAPP_and_MAPPFinder_Protocols | This page gives a sample protocol for the analysis of a ''Vibrio cholerae'' dataset.]] | |||
* You will keep a detailed electronic notebook page that details all of the data manipulations and calculations that you perform on your dataset. | |||
* You will upload the following list of files (note that it may be easier to zip all of these files together and then upload them as a single zipped file, rather than zipping and uploading individually, for filetypes not allowed by OpenWetWare). | |||
*# Your exceptions file when you imported your data into GenMAPP: <code>.EX.txt</code> | |||
*# Your Expression Dataset file: <code>.gex</code> | |||
*# Your GO results files: <code>XXX-CriterionX-GO.txt</code> | |||
*# Your GO results saved as Excel spreadsheets with filters applied: <code>.xls</code> or <code>.xlsx</code> | |||
*# The MAPP you looked at: <code>.mapp</code> | |||
*# The MAPPFinder GO mappings file: <code>.gmf</code> | |||
'''Note:''' The individual journal entry for this week is worth 10 points like all other journal entries. The research presentation is worth 80 points. |
Revision as of 16:32, 29 October 2014
This journal entry is due on Wednesday, December 10 at midnight PDT (Tuesday night/Wednesday morning). NOTE that the server records the time as Eastern Daylight Time (EDT). Therefore, midnight will register as 03:00.
NOTE that this assignment is UNDER CONSTRUCTION.
Background
References
- Brown, P.O. & Botstein, D. (1999) Exploring the new world of the genome with DNA microarrays Nature Genetics 21: 33-37.
- Campbell, A.M. and Heyer, L.J. (2003), “Chapter 4: Basic Research with DNA Microarrays”, in Discovering Genomics, Proteomics, and Bioinformatics, Cold Spring Harbor Laboratory Press, pp. 107-124. (Available on MyLMUConnect)
- Dahlquist, K.D., Salomonis, N., Vranizan, K., Lawlor, S.C., & Conklin, B.R. (2002) GenMAPP, A New Tool for Viewing and Analyzing Microarray Data on Biological Pathways. Nature Genetics 31: 19-20.
- DeRisi, J.L., Iyer, V.R., and Brown, P.O. (1997) Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale. Science 278: 680-686.
- Doniger et al. (2003)
- Salomonis et al. (2007)
Overview of DNA Microarray Analysis
This is a list of steps required to analyze DNA microarray data.
- Quantitate the fluorescence signal in each spot in the microarray image.
- Typically performed by the scanner software, although third party software packages do exist.
- The image of the microarray slide and this quantitation are considered the "raw-est" form of the data.
- Ideally, this type of raw data would be made publicly available upon publication.
- In practice, the image data is usually not made available because the raw image file of one slide could be up to 100 MB in size.
- Also, some journals do not require data deposition as a requirement for publication, so often published data are not actually available anywhere for download.
- Microarray data is not centrally located on the web. Some major sources are:
- NCBI GEO
- EBI ArrayExpress
- Stanford Microarray Database
- PUMAdb (Princeton Microarray Database)
- In addition, microarray data can sometimes be found as supplementary information with a journal article or on an investigator's own web site.
- Calculate the ratio of red/green fluorescence
- Log(base 2) transform the ratios
- Normalize the log ratios on each microarray slide
- Normalize the log ratios for a set of slides in an experiment
- Perform statistical analysis on the log ratios
- Compare individual genes with known data
- Look for patterns (expression profiles; clusters) in the data (many programs are available to do this)
- Perform Gene Ontology term enrichment analysis (we will use MAPPFinder for this)
- Map onto biological pathways (we will use GenMAPP for this)
Individual Journal Assignment
- Store this journal entry as "username Week 15" (i.e., this is the text to place between the square brackets when you link to this page).
- Create the following set of links. These links should all be in your personal template; then use the template on your journal entry.
- 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 "BIOL368/F14" category to the end of your wiki page.
Complete Microarray Data Analysis
- Using the spreadsheet that you submitted for the Week 13 Assignment, you will now complete GenMAPP and MAPPFinder analysis of your dataset.
- You will keep a detailed electronic notebook page that details all of the data manipulations and calculations that you perform on your dataset.
- You will upload the following list of files (note that it may be easier to zip all of these files together and then upload them as a single zipped file, rather than zipping and uploading individually, for filetypes not allowed by OpenWetWare).
- Your exceptions file when you imported your data into GenMAPP:
.EX.txt
- Your Expression Dataset file:
.gex
- Your GO results files:
XXX-CriterionX-GO.txt
- Your GO results saved as Excel spreadsheets with filters applied:
.xls
or.xlsx
- The MAPP you looked at:
.mapp
- The MAPPFinder GO mappings file:
.gmf
- Your exceptions file when you imported your data into GenMAPP:
Note: The individual journal entry for this week is worth 10 points like all other journal entries. The research presentation is worth 80 points.