Jennifer Okonta Week 9
- Since i missed class on tuesday, i set up a meeting with Dr. Dahlquist and completed my assignmen with Andrew H. as my partner.
- First, I downloaded Andrew Forney spreadsheet becuase his spreadsheet was the best one.
- Then I was assigned the old database to use.
- Next, I started up the GenMapp program
- I clicked Data and chose the the VC cholerae file that Andrew forney created.
- Next i clicked the Expression Data Manager from the drop down box.
- Then i uploaded my text file and allowed the program to convert it.
- After waiting a couple of minutes the file was finally converted and i got my results.
There were 722 errors found and compared to the new database that had 121 which shows that the new database has found more information about the missing genes that were listed as errors in the old database.
- Next i customized my expression data sheet.
- I chose the LogFC_All, named it increased, chose a light green color with a value > 0.25 AND [Pvalue] < 0.05.
- Next I i named the other one decreased with the color pink and chose Avg_LogFC_all with the velue < -0.25 AND [Pvalue] < 0.05.
- Then I saved it.
- Next I launched MAPP Fnder.
- Then I calculated my results.
The Top Ten Ontology Terms
Amino Acid Metabolic Process
Cellular molecule biosynthesis process
Cellular nitrogen compound metabolic process
Cellular amine metabolic process
Cellular amino acid derivative metabolic process
Cellular biopolymer biosynthetic process
Biopolymer biosynthetic process
Cell projection organization
- Next I searched for the genes by putting their names in the Gene Id Box
VC0647- 3'-5' exoriboniclueose activity, transferase activity and nucleotidyltransferase activity
VCA0583- transport, outer membrane bound periplasmic space
These are not the same results as the new one becuase the new GenMapp can identify more genes then the old one becase more information has been found about these genes.
- I clicked the VCA058
- I clicked the outer membrane-bounded periplasmic space
- I then clicked on the uniprot link and found the name which was Q9KM06-VIBCH- no criteria was met which means there was no increase or decrease. This genes is involved in catalytic activity, dihydroxy-acid dehydratase activity, metabolic processes, and cellular amino acid biosynthetic process.
- Next i did the excel part for comparison.
- There were 339 probes met the [Avg_LogFC_all] > 0.25 AND [Pvalue] < 0.05 criteria for both new and old.
- 291 probes linked to UniProt compared to 338
- 184 probes linked to a GO term when compared to 219
- 5221 probes linked to the datas et which is the same between the two.
- 4490 linked to uniprot ID when compared to the 5100.
- 1190 linked to the Go terms when compared to the 2475 found using the new genmapp
- N=1990 and R =184