Revision as of 23:50, 23 October 2015

Electronic Lab Notebook

• All Files for Week 8 Journal

Statistical Analysis of Vibrio cholerae Microarray Data (Part 1)

MAPPFinder Analysis of Vibrio cholerae Microarray Data (Part 2)

Reminders

• Finish the Sanity Check
• I used the 2010 Vibrio Cholera database

• When uploading my tab delimited file to the GenMAPP software for conversion, 121 errors were detected in my raw data.
• My partner, Brandon L., had 772 errors detected in his raw data conversion while using the 2009 Vibrio Cholera database.
  • This difference in errors is most likely due to the extensiveness of our databases. Because Brandon was using an older version of the database while I was using a newer version, it is possible that his version had fewer genes than mine.
• We produced our color set to indicate increased expression.
• Top 10 Gene Ontology Results:
  1. branched chain family amino acid metabolic process
  2. branched chain family amino acid biosynthetic process
  3. IMP metabolic process
  4. IMP biosyntehtic process
  5. purine ribonucleoside monophosphate metabolic process
  6. purine nucleoside monophosphate metabolic process
  7. purine nucleoside monophosphate biosyntehtic process
  8. purine ribonucleoside monophosphate biosyntehtic process
  9. arginine metabolic process
  10. ccellular nitrogen compound biosynthetic process
• Searching through MAPPFinder for published genes:
  • VC0028: metal ion binding, iron-sulfur cluster binding, 4 iron 4 sulfur cluster binding, catalytic activity, lyase activity
  • VC0941: pyridoxal phosphate binding, catalytic activity, transferase activity, glycine hydroxymethyltransferase activity
  • VC0869: nucleotide binding, ATP binding, catalytic activity, lyase activity
  • VC0051: nucleotide binding, ATP binding, catalytic activity, lyase activity, carboxy-lyase activity
  • VC0647: 3'-5'-exoribonuclease activity, transferase activity, nucleotidyltransferase activity, polyribonucleotide nucleotidyltransferase activity
  • VC0468: metal ion binding, nucleotide binding, ATP binding, catalytic activity, ligase activity, glytathione synthase activity
  • VC2350: catalytic activity, lyase activity, deoxyribose-phosphate aldolase activity
  • VCA0583: outer membrane-bounded periplasmic space
• The GO term I clicked on was outer membrane-bounded periplasmic space
  • The gene I was looking for was VCA0583, which translated to Q9KM06 on Uniprot
  • This gene did not have a significant change in expression
  • This gene is responsible for transporter activity, transport, and outer membrane-bounded periplasmic space
• TODO:Look at the top of the spreadsheet. There are rows of information that give you the background information on how MAPPFinder made the calculations. Compare this information with your partner who used a different version of the Vibrio Gene Database. Which numbers are different? Why are they different? Record this information in your individual journal entry.
• TODO:Interpret your results. Look up the definitions for any GO terms that are unfamiliar to you. The "official" definitions for GO terms can be found at http://www.geneontology.org. You can use one of the online biological dictionaries as a supplement, if needed. Write a paragraph relating the results of this GO analysis to the experiment performed (comparing laboratory-grown and patient-derived Vibrio cholerae. You need to give a biological interpretation of what do each of these GO terms in your filtered list have to to with the pathogenecity of the bacterium? You may consult with your partner on this, but your explanation on your individual journal page needs to be in your own words. This is where the real "brain power" comes in with interpreting DNA microarray data. Even experienced scientists struggle with this part. Use your creativity as a scientist to stretch your brain in this question.

Other Links

User Page: Anindita Varshneya
Class Page: BIOL/CMSI 367: Biological Databases, Fall 2015
Group Page: GÉNialOMICS

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