MSymond1 Week 10

media:Symonds_Week10_Profiles.zip media: Symonds_week_10Golist.zip media:Symonds_Miller_STEM_Presentation.pptx

1. I chose profile 9 because it has very dynamic lines and a wide range of values across all of the lines.
   • There are 200 genes assigned to this profile
   • There are 60.3 genes expected to belong to this profile
   • The p-value for this profile is 3.1E-48
   • 28 GO terms are associated with a p-value of less than .05, and 4 GO terms are associated with a p-value of less than .05
     • vesicle-mediated transport (GO:0016192): A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
     • Golgi apparatus (GO:0005794): A membrane-bound cytoplasmic organelle of the endomembrane system that further processes the core oligosaccharides (e.g. N-glycans) added to proteins in the endoplasmic reticulum and packages them into membrane-bound vesicles. The Golgi apparatus operates at the intersection of the secretory, lysosomal, and endocytic pathways.
     • cytoplasmic translation (GO:0002181): The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.
     • protein transport (GO:0015031): The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
     • ribosomal small subunit assembly (GO:0000028): The aggregation, arrangement and bonding together of constituent RNAs and proteins to form the small ribosomal subunit.
     • transaminase activity (GO:0008483): Combining with the neurotransmitter dopamine and activating adenylate cyclase via coupling to Gi/Go to initiate a change in cell activity.
2. The YEASTRACT results
   • 25 of the genes were green and significant
   • media:Symonds_YEASTRACTresults.xlsx
   • Yes, CIN5 is in the table, 39.00% is in user set, 3.39% is in scerevisiae, and the p-value is 0.005141327836732. GLN3 is also in the database, 34.00% is in the user set, 2.76% is in scerevisiae, and the p-value is 0.346793143826899.
3. GRNsight results
   • I decided which genes to include by using the genes with the smallest p-values on my chart, I added them to the network in order from least to greatest, all of the p-values were at most E-5.
   • My network had 19 genes and 41 edges.
   • 

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