Samanhta M. Hurndon Week 14: Final Project
- Table of significant genes at p< 0.05,0.01,0.001
- Top ten significant genes
- Top ten increased/decreased GO terms
- Make a list of the functions of the top ten genes.
- Take all of this data and hypothesize why under the conditions of the experiment they would be up or down regulated.
- How do your top ten significant genes relate to the GO terms? How do they relate to the experimental conditions?
- How do your results and hypothesis align with the paper you read?
Top 10: Decreased GO Terms
- ribosome: Cellular Component .An intracellular organelle, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). 
- structural molecule activity: Molecular Function. The action of a molecule that contributes to the structural integrity of a complex or assembly within or outside a cell. 
- protein metabolic process: Biological Process. The chemical reactions and pathways involving a specific protein, rather than of proteins in general. Includes protein modification. 
- cytoplasm: Cellular Component. All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. 
- organelle part: Cellular Component. Any constituent part of an organelle, an organized structure of distinctive morphology and function. Includes constituent parts of the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, but excludes the plasma membrane. 
- cellular homeostasis: Biological Process. Any process involved in the maintenance of an internal steady state at the level of the cell. 
- pathogenesis: Biological Process. The set of specific processes that generate the ability of an organism to cause disease in another. .
- fatty acid biosynthetic process: Bological Process. The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes. 
- ATP synthesis coupled proton transport: Biological Process. The transport of protons across a membrane to generate an electrochemical gradient (proton-motive force) that powers ATP synthesis. 
- nickel ion binding. Molecular Function. Interacting selectively and non-covalently with nickel (Ni) ions. 
Top 10: Increased GO Terms
- regulation of gene expression, epigenetic: Biological Process. Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence.
- Intracellular. Cellular Component. 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. 
- membrane part: Cellular Component. Any constituent part of amembrane, a double layer of lipid molecules that encloses all cells,and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
- macromolecule modification: Cellular Component. Any constituent part of a membrane, a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
- cellular nitrogen compound metabolic process: Cellular Component.The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells.
- iron-sulfur cluster binding: Molecular Function. Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
- response to stress: Biological Process. Any process that results in a change in state or activity of a cell or an organism(in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis,usually, but not necessarily, exogenous (e.g. temperature, humidity,
- transport: Biological Process. The directed movement of substances(such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. 
- carbohydrate biosynthetic process: Biological Process. The chemical reactions and pathways resulting in the formation of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. 
- nucleoside-triphosphatase activity: Molecular Function. Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
Overall: Top Ten Regulated Genes
* HP1555 – Elongation Factor Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF-Tu.GTP complex up to the GTP hydrolysis stage on the ribosome * HP1557 - Flagellar hook-basal body protein FliE * HP0912 – Predicted to be an outer membrane protein * HP1203 - Transcription antitermination protein * HP0601- Flagellin A Part of the Flagellar assembly and affects motility * HP1429 – Predicted to be a polysialic acid capsule expression protein * HP0962 - Acyl carrier protein * HP1427 – Predicted to be a histidine and glutamine-rich metal binding protein * HP1210 - Serine acetyltransferase * HP0264 – Predicted to be an ATP-dependent chaperone protein ClpB
References are in the same order as their respective genes
* http://www.uniprot.org/uniprot/P55975. Dec 6th, 2011. * http://www.genome.jp/dbget-bin/www_bget?hpy:HP1557. Dec 6th, 2011. * http://combrex.bu.edu/DAI?command=SciBay&fun=gene&geneID=899441. Dec 6th, 2011. * http://www.genome.jp/dbget-bin/www_bget?hpy+HP1203. Dec 6th, 2011. * http://www.genome.jp/dbget-bin/www_bget?hpy:HP0601. Dec 6th, 2011. * http://combrex.bu.edu/DAI?command=SciBay&fun=gene&geneID=899866. Dec 6th, 2011. * http://www.gene-profiles.org/gene/hp0962-helicobacter-pylori-26695-899495. Dec 6th, 2011. * http://combrex.bu.edu/DAI?command=SciBay&fun=gene&geneID=899868. Dec 6th, 2011. * http://www.genome.jp/dbget-bin/www_bget?hpy:HP1210. Dec 6th, 2011. * http://combrex.bu.edu/DAI?command=SciBay&fun=gene&geneID=899187. Dec 6th, 2011.