Salomon Garcia: Lab notebook Week 9

Week 9 Notes
[[Media:Data_for_use_of_Genmapp_and_mappfinder_Salomon_Garcia_Valencia.zip| Data for GenMAPP and MAPPFinder]]
 * total number of errors found while using the old database was a total of 772 genes. This is due to having different versions of the database and using the different database so as expected the older version will have more errors compared to that of the newer version.
 * For this assignment I chose the old database from fall 2008 and my partner and I are running the decreased portion of the assingment and the file being uploaded is for dataset just in case computer fails.

List of top ten gene ontology that were listed:
 * 1) oxidoreductase activity
 * 2) carbon-carbon lyase activity
 * 3) chorismate metabolic process
 * 4) aromatic amino acid family biosynthetic process
 * 5) dicarboxylic acid metabolic process
 * 6) transcription elongation regulator activity
 * 7) outer membrane
 * 8) aromatic amino acid family metabolic process
 * 9) lyase activity
 * 10) naphthoate syntase activity


 * Our gene ontology search terms ended up being quite different as a matter of fact not one single term matched and this is because the databases are so different and the newer databases have more recent information.


 * The gene that I clicked on was the transport gene. That gene was a transport gene that showed many changes throughout the process in GenMapp and Mappfinder


 * VC0028
 * There were no go terms associated with this id


 * VC0941
 * There were no go terms associated with this id


 * VC0869
 * There were no go terms associated with this id


 * VC0051
 * There were no go terms associated with this id


 * VC0647
 * 3'-5'-exoribonuclease activity
 * transferase activity
 * nucleotidytransferase activity


 * VC0468
 * There were no go terms associated with this id


 * VC2350
 * There were no go terms associated with this id


 * VCA0583
 * transport
 * outer membrane-boundedperiplasmic space

Link to the information that was used in class: [[Media:Salomon_Garcia_week_9.zip| Week 9 material]]

78 probes met the [Avg_LogFC_all] < -0.25 AND [Pvalue] < 0.005 criteria. 61 probes meeting the filter linked to a UniProt ID. 41 genes meeting the criterion linked to a GO term. 5221 Probes in this dataset 4449 Probes linked to a UniProt ID. 1990 Genes linked to a GO term. The z score is based on an N of 1990 and a R of 41 distinct genes in the GO.
 * All of the numbers were different from my partner and my statistical analysis. This as mentioned earlier could be due to using different databases.
 * These were the numbers seen from the old database:

578 probes met the [Avg_LogFC_all] < -0.25 AND [Pvalue] < 0.05 criteria. 565 probes meeting the filter linked to a UniProt ID. 330 genes meeting the criterion linked to a GO term. 5221 Probes in this dataset 5100 Probes linked to a UniProt ID. 2475 Genes linked to a GO term. The z score is based on an N of 2475 and a R of 330 distinct genes in the GO.
 * Theses were the numbers seen from the new database:


 * After the data was further filtered there were about 7 or 8 terms that matched the filters and here is the link to the excel sheet. Link:[[Media:Decreased-Criterion1-GO_with_analysis.xls|Filtered data]]


 * Most of the GO terms are closely related they deal with metabolic processes that are used by Vibrio Choloerae. There were three terms that deal with some activities and membrane activities as well.