Andrew Forney Week 9

Author: Andrew Forney

Assignment: Individual Journal 9

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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

This process follows the steps described in the protocol; more specifically, the MAPPFinder application was used to analyze the expression dataset and yielded the following relations:

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

MAPP Finder's GO relation was used to find associated functions with the following genes:

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

The spectrum of information covered by Andrew's output was much greater; here, most were not found because I was working from an older database. Conversely, Andrew had the up-to-date database in which more information regarding pathways and GO relations had been discovered, and so he was able to uncover more about the functionality.

GenMAPP Examination: VCA0583

Further examination of the VCA0583 transport function allowed functional pathway analysis using GenMAPP.

Uniprot ID: Q9KM06_VIBCH

Gene Ontology Analyzed: transport

Significantly different?: No, p = 0.1011 > 0.05

Functions: (Putative uncharacterized protein)

• Technical Term: Complete proteome
• Cellular Component: outer membrane-bounded periplasmic space
• Molecular function: transport and transporter activity

Criterion0 Excel Juxtaposition

Comparing our two excel headers yielded several differences, and some similarities. Here was the summary, with explanations after each:

• '339 probes met the [Avg_LogFC_all] > 0.25 AND [Pvalue] < 0.05 criteria. The number here was the same between files.
• 291 probes meeting the filter linked to a UniProt ID. Here, Andrew had a superior amount: 338
• 184 genes meeting the criterion linked to a GO term. Here, Andrew had a superior amount: 219
• 5221 Probes in this dataset The number here was the same between files.
• 4449 Probes linked to a UniProt ID. Here, Andrew had a superior amount: 5100
• 1990 Genes linked to a GO term. Here, Andrew had a superior amount: 2475
• The z score is based on an N of 1990 and a R of 184 distinct genes in the GO. Here, Andrew's N = 2475, R = 219.

Again, these observed differences can be reconciled by the fact that Andrew was working with a more up-to-date database with more genetic information. Note that all of the differences were positively favoring Andrew's data because there was more to analyze.

Criterion0 VCA0583 Excel Filter and Definitions

Four significant results were obtained from the filtering of the Criterion0 file. Two were observed via MAPPFinder to have a parent-child relationship: cell projection organization > flagellum organization.

Here is a list of the results along with a definition provided by Gene Ontology:

1. Cell projection organization: (GOID: 0030030) A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
2. Flagellum organization: (GOID: 0043064) A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a flagellum, a long thin projection from a cell, used in movement.
3. Magnesium ion binding: (GOID: 0000287) Interacting selectively and non-covalently with magnesium (Mg) ions.
4. Extracellular region: (GOID: 0005576) The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Criterion0 VCA0583 Analysis

Because our analysis was based on the up-regulated differences from the experiment, we are observing the functions that increased in prevalence after the specific gene, VCA0583, was removed. As such, it is logical to conclude that this gene was an inhibitor for the four factors that we note above. This is interesting because, with regard to the first two characteristics, it would seem that flagellal development is a desirable feature for an infectious bacteria to have (in order to move and infect other organisms).

Perhaps this inhibition, then, relates to (as the definition states) a disassembly of the flagella, meaning the gene is involved in an inhibition of the disasembly--i.e. that it prevents the disassembly of the flagella. This concept seems to go along with the first function found: "Cell projection organization," which seems to include flagellum organization as a subset.

Magnesium ion binding inhibition seems to be less of an intuitive explanation as to its role in making the organism pathogenic. After some research on the topic, I discovered that viruses must bind to other cells before infecting them. Several papers in the field allude to magnesium ions inhibitting the binding of viruses to their host cell. If this is the case, then the virus would want to avoid binding to magnesium ions in order to correctly bind to a host cell, thus explaining the inhibitory function of the gene on this point.

As per the extracellular region inhibition of a host cell with an intracellular parasite, it makes sense that the infectious organism would want to compromise the integrity of the surrounding host cell material in order to suit the environment to its liking. The definition here is rather vague though, and so it might simply be unclear as to the exact influence that the gene in question has in this regard.

In summary, it appears that VCA0583's role in making Vibrio Colerae pathogenic centers primarily on its movement and binding capabilities, with perhaps a little focus on its infectious function after binding.

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