BIOL368/F14:Week 15
From OpenWetWare
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.