Andrew Forney Week 9: Difference between revisions

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Andrew H and I followed the instructions afforded by the protocol, using my text file computed in the previous assignment. After defining our expression set, the following results were observed:
Andrew H and I followed the instructions afforded by the protocol, using my text file computed in the previous assignment. After defining our expression set, the following results were observed:


* The number of errors discovered in the output was: 772
* The number of errors discovered in the output was: 772. These all provided the error message: "Gene not found in OrderedLocusNames or any related system."
* The number of errors on my database, the older version, was far greater--772 compared to 121 for Andrew H. Most likely, this is because more genomic information for the vibrio colerae species exists in a more up-to-date database, and as such, more recently-defined proteins were found in Andrew's case than in mine.
* The number of errors on my database, the older version, was far greater--772 compared to 121 for Andrew H. Most likely, this is because more genomic information for the vibrio colerae species exists in a more up-to-date database, and as such, more recently-defined proteins were found in Andrew's case than in mine.


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=====MAPPFinder Procedure=====
=====MAPPFinder Procedure=====


Top ten GO terms:
'''Top ten GO terms:'''
# Macromolecule metablic process
# Macromolecule metablic process
# Localization
# Localization
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# Flagellum organization
# Flagellum organization
# Cellular biopolymer metabolic process
# Cellular biopolymer metabolic process
These terms differ significantly between Andrew's output and mine. This is likely because the quantity of genetic information available to Andrew was much greater, and as such, different pathways (or even the same pathways with different quantitative values) could have been analyzed and so yielded different results.
'''Individual Gene-GO Relations'''
# ''VC0028:'' No MAPPs or GO terms could be found.
# ''VC0941:'' No MAPPs or GO terms could be found.
# ''VC0869:'' No MAPPs or GO terms could be found.
# ''VC0051:'' No MAPPs or GO terms could be found.
# ''VC0647:'' mRNA catabolic process, RNA processing, cytoplasm, RNA binding, 3'-5' exoribonuclease activity, transferase activity, nucleotidyltransferase activity, polyribonucleotide nucleotidyltransferase activity
# ''VC0468:'' No MAPPs or GO terms could be found.
# ''VC2350:'' No MAPPs or GO terms could be found.
# ''VCA0583:'' transport, outer-membrane bounded periplasmic space, transporter activity




Revision as of 18:42, 26 October 2010

Author: Andrew Forney

Assignment: Individual Journal 9

Electronic Lab Notebook: Week 9

GenMAPP Expression Dataset Manager Procedure

Andrew H and I followed the instructions afforded by the protocol, using my text file computed in the previous assignment. After defining our expression set, the following results were observed:

  • The number of errors discovered in the output was: 772. These all provided the error message: "Gene not found in OrderedLocusNames or any related system."
  • The number of errors on my database, the older version, was far greater--772 compared to 121 for Andrew H. Most likely, this is because more genomic information for the vibrio colerae species exists in a more up-to-date database, and as such, more recently-defined proteins were found in Andrew's case than in mine.


MAPPFinder Procedure

Top ten GO terms:

  1. Macromolecule metablic process
  2. Localization
  3. Cell projection organization
  4. Cellular macromolecule metabolic process
  5. Transporter activity
  6. Biopolymer metabolic process
  7. Cellular biopolymer metabolic process
  8. Macromolecule biosyntheic process
  9. Flagellum organization
  10. Cellular biopolymer metabolic process

These terms differ significantly between Andrew's output and mine. This is likely because the quantity of genetic information available to Andrew was much greater, and as such, different pathways (or even the same pathways with different quantitative values) could have been analyzed and so yielded different results.


Individual Gene-GO Relations

  1. VC0028: No MAPPs or GO terms could be found.
  2. VC0941: No MAPPs or GO terms could be found.
  3. VC0869: No MAPPs or GO terms could be found.
  4. VC0051: No MAPPs or GO terms could be found.
  5. VC0647: mRNA catabolic process, RNA processing, cytoplasm, RNA binding, 3'-5' exoribonuclease activity, transferase activity, nucleotidyltransferase activity, polyribonucleotide nucleotidyltransferase activity
  6. VC0468: No MAPPs or GO terms could be found.
  7. VC2350: No MAPPs or GO terms could be found.
  8. VCA0583: transport, outer-membrane bounded periplasmic space, transporter activity



Assignment Files

  • PENDING Everything uploaded
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