J'aime C. Moehlman's Week 13

GenMAPP Expression Dataset Manager Procedure

 * There were 772 errors detected in the raw data for V. cholerae, thus they were not not converted.
 * We then created a color sets based off of set criteria.
 * We uploaded it onto lionshare in order to save it.
 * Ran the MAPPFinder for our two criteria; criteria one is based on the average FC of all being greater than .25 and pvalue is less than .05. Criteria 2 says the average is less than -.25 and less than .05.
 * top 10 gene ontology:
 * 1) protein folding
 * 2) unfolded protein binding
 * 3) cytoplasm
 * 4) cis-trans isomerase activity
 * 5) peptidyl-prolyl-cis-trans isomerase activity
 * 6) chorismate metabolic process
 * 7) aromatic amino acid family biosynthetic process
 * 8) protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
 * 9) phosphoenolpyruvate-dependent sugar phosphotransferase system
 * 10) intracellular part

EX: (increased) glycolysis has 10 enzymes, 10 genes. filtering: pvalue z score number changed percent changed
 * there is an increase in expression, and also a decrease in expression; finding the GO terms associated with both inc. and dec.; they each have a process(ex: glycolysis), component(location in cell), and function(type of enzyme)
 * what processes are involved in making vc pathogenic?

specific GO terms for Genes mentioned by Merrell

 * VC0028- not found
 * VC0941- not found
 * VC0869- not found
 * VC0051- not found
 * VC0647- biological processes- mRNA catabolic processes, bilogical processes- RNA processing, cellular component-cytoplasm, molecular function- RNA binding, catalytic activity-3'5'exoribonuclease activity, catalytic activity-transferase activity, catalytic activity-nucleotidyltransferase activity, catalytic activity-polyribonucleotide nucleotidyltransferase activity
 * VC0468- not found
 * VC2350- not found
 * VCA0583- establishment of localization- transport, cellular component- envelope (cell envelope) outermembrane bounded periplasmic space, molecular function- transport activity
 * Clicked on mRNA catabolic process for Gene VC0647- and it showed genes: 1 (PNP_VIBCH) showed decreased expression and the other (CSRA_VIBCH) showed no change.
 * The mRNA catabolic process backpage shows that the function mRNA breakdown or catabolism. This is the chemical reactions and pathways resulting in the breakdown of mRNA.

Biological Processes

 * 1) protein folding: The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
 * 2) chorismate metabolic process: The chemical reactions and pathways involving chorismate, the anion of (3R-trans)-3-((1-carboxyethenyl)oxy)-4-hydroxy-1,5-cyclohexadiene-1-carboxylic acid.
 * 3) aromatic amino acid family biosynthetic process:The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
 * 4) phosphoenolpyruvate-dependent sugar phosphotransferase system:The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC.

Molecular Function

 * 1) unfolded protein binding: Interacting selectively and non-covalently with an unfolded protein.
 * 2) cis-trans isomerase activity: Catalysis of a reaction that interconverts cis and trans isomers. Atoms or groups are termed cis or trans to one another when they lie respectively on the same or on opposite sides of a reference plane identifiable as common among stereoisomers.
 * 3) protein-N(PI)-phosphohistidine-sugar phosphotransferase activity: Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sugar(out) = protein histidine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport.
 * 4) peptidyl-prolyl-cis-trans isomerase activity: Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).

Cellular Component

 * 1) cytoplasm: All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
 * 2) intracellular part:Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Definitions found at: www.geneontology.org

MAPPFinder Criterion

 * [[Media:Vc MAPPFinder Results 3-Criterion0-GO.xls|Increased]]
 * [[Media:Vc MAPPFinder Results 3-Criterion1-GO.xls|Decreased]]

The genes which had increased expression were those which played a part in the overall organization of the bacterial cell, and those for synthesis of RNA nucleotides, specifically the purine bases, adenine and guanine. These two ribonucleotides play a large role in energy distribution within the bacteria, in the forms of ATP and GTP. GTP is especially useful in terms of cytoskeletal rearrangement, whereas ATP is a more general energy molecule. The genes which had decreased expression all had to deal with the buildup of sugars, especially genes for the construction of long term storage molecules, like starches. This makes a lot of sense, as the cell would need to utilize all of its stored energy while virulent. Also, there is some decrease in translation, in that the bacteria is less 'concerned' with protein synthesis and is more focused on making itself infectious.
 * remember that it'll be the opposite because its decreased on yours

Presentation
[[Media:Bioinformatics Microarray Data Project.ppt|Powerpoint]]

[[Media:Bioinformatics Microarray Data Project FINAL.ppt|New Powerpoint]]