Michael R. Pina Week 13

Running GenMAPP and MAPPFinder
Everything went fairly smoothly except for crash near the end of my processing. I received 1778 errors all with the same message "Gene not found in TAIR or any related system. " so I think it is safe to ignore these for now.

[[Media:Mpina_VanDeMortel_Scaled_Centered.EX.txt|EX.txt file]]

Filtered results from Excel
[[Media:Mpina Results for TCAT-Criterion0-GO.xls|Criterion 0 Filtered]]

[[Media:Mpina Results for TCAT-Criterion1-GO.xls|Criterion 1 Filtered]]

Criterion 0

 * terpenoid metabolic process
 * cell surface receptor linked signal transduction
 * anchored to plasma membrane
 * response to starvation
 * intrinsic to plasma membrane
 * isoprenoid metabolic process
 * serine family amino acid metabolic process
 * response to nutrient levels
 * response to salicylic acid stimulus
 * response to extracellular stimulus
 * protein binding
 * protein import
 * mRNA processing
 * response to jasmonic acid stimulus
 * methyltransferase activity
 * transferase activity, transferring one-carbon groups
 * protein targeting

These are the results for upregulated processes. Many activities related to terpenoids are involved here. I did some digging around to see what the role of terpenoids in plants are and found that terpenoids are sometimes added to proteins to increase attachment to cell membranes. Because of this (and because of other processes like protein binding) I am gathering that the plant is trying to pump out as much zinc as possible using membrane proteins.

Criterion 1

 * extracellular region
 * lipid catabolic process
 * chromatin modification
 * establishment or maintenance of chromatin architecture
 * glutamine family amino acid metabolic process
 * covalent chromatin modification
 * pyridoxal phosphate binding
 * regulation of gene expression, epigenetic
 * regulation of gene expression
 * hydrolase activity, acting on ester bonds
 * chromosome organization
 * regulation of macromolecule metabolic process
 * jasmonic acid mediated signaling pathway
 * two-component response regulator activity
 * nucleosome
 * vitamin binding
 * regulation of transcription
 * histone modification
 * histone-lysine N-methyltransferase activity
 * protein-lysine N-methyltransferase activity
 * lysine N-methyltransferase activity
 * DNA binding

A lot of this related to chromosomes and more specifically chromatin appear to be downregulated. I suspect that the toxicity of the zinc could be interfering with these processes which is what makes it harmful. Also interesting is that lipid catabolic process is downregulated because terpenoids are lipids so this shows that the plant is trying to conserve them for attaching to proteins.

I didn't see a things related to lignin biosynthesis in my results but this is likely due to the fact that we compared the plants under different conditions in relation to the paper.