KP Ramirez Week 13

Running GenMAPP
This began when i finished formatting my excel sheet and converting it into a Tab-Delimited txt file. After this I launched the GenMAPP program and loaded my Gene Database HS. This was followed by using the expression dataset menu and selecting my tab delimited file. After this GenMAPP began converting the raw expression data.

My number of errors was 1792

The next step was labeling in the legend how we were corresponding our data into GenMAPP. Since we were working with 4 different folds: This corresponded to 8 different criteria on the Expression dataset manager.
 * HvsPG, MetvsPG, HvsMet, and AIvsPG.

Ex
 * Increased HvsPGfold >.25 AND HvsPGTtest <.05
 * Decreased HvsPGfold <-.25 AND HvsPGTtest <.05

Color Legend

 * HvsPGfold Increased =Red Opposite Decreased=Green
 * MetvsPGfold Increased=Brown Opposite Decrease=Light blue
 * HvsMetfold Increased=Orange Opposite Decreased=Light green
 * AlVsPGfold increased=Purple Opposite Decreased=Blue
 * Grey no criteria

Criterion 0-7
After this i ran MappFinder. Checking off "Gene Ontology" and "P value" as well as uploading the .gex file on the Lionshare website.
 * [[Media:IncHvsPgFold-Criterion0-GO.txt|Criterion 0 Increased H vs PG Fold]]
 * [[Media:DecHvsPgFold-Criterion1-GO.txt|Criterion 1Decreased H vs PG Fold]]
 * [[Media:IncMetvsPGFoldCriterion2-GO.txt| Criterion 2 Increased Met vs PG Fold]]
 * [[Media:DecMetvsPGFold-Criterion3-GO.txt| Criterion 3 Decreased Met vs Pg Fold]]
 * [[Media:IncHvsMetFold-Criterion4-GO.txt| Criterion 4 Increased H vs Met Fold]]
 * [[Media:DecHvsMetFold-Criterion5-GO.txt| Criterion 5 Decreased H vs Met fold]]
 * [[Media:IncAIvsPGFOLD-Criterion6-GO.txt| Criterion 6 Increased AI vs PG fold]]
 * [[Media:DecAIvsPGfold-Criterion7-GO.txt| Criterion 7 Decreased AI vs Pg fold]]

Top 10 Results
Criterion 0
 * 1) Regulation of retinal programmed cell death
 * 2) Neutrophil chemotaxi
 * 3) IgE binding
 * 4) Cell Surface
 * 5) Leukocye chemotaxis
 * 6) Defense response
 * 7) Peptidoglycan metabolic process
 * 8) Response to wounding
 * 9) MAPKKK Cascade
 * 10) Inflammatory response

Criterion 1
 * 1) Nucleosome
 * 2) Nucleosome assembly
 * 3) Chromatin assembly
 * 4) Chromatin assembly or dissaembly
 * 5) Cysteine biosynthetic process
 * 6) Protein carrier activity
 * 7) Protein DNA conplex assembly
 * 8) Chromatin
 * 9) Chromasomal part
 * 10) chromosome

Criterion 2
 * 1) M phase
 * 2) M phase of mitotic cell cycle
 * 3) Mitosis
 * 4) Cell Cycle phase
 * 5) Cell Division
 * 6) Mitotic Cell Cycle
 * 7) Spindle
 * 8) Cell Cycle Checkpoint
 * 9) Spindle organization and biogenesis
 * 10) Cell Cycle

Criterion 3
 * 1) Muscle contraction
 * 2) Extracellular region
 * 3) Sarcomere
 * 4) Extracellualr region part
 * 5) Contractile fiber part
 * 6) Regulation of muscle contraction
 * 7) Multicellular organismal process
 * 8) Monooxygenase activity
 * 9) Oxidoredcutase activity
 * 10) Anatomical structure development

Criterion 4
 * 1) Muscle contraction
 * 2) Multicellular organismal process
 * 3) Smooth muscle contraction
 * 4) Regulation of muscle contraction
 * 5) Anatomical structure development
 * 6) Extracellular region
 * 7) Multicellular organismal development
 * 8) Extracellular region part
 * 9) System development
 * 10) Regulation of multicellular organisms

Criterion 5
 * 1) Integral to plasma membrane
 * 2) Intrinsic to plasma membrane
 * 3) Cell communication
 * 4) Plasma membrane
 * 5) Plasma membrane part
 * 6) Signal transduction
 * 7) Receptor activity
 * 8) G-protein coupled receptor activity
 * 9) Molecular tranducer activity
 * 10) Signal transducer activity

Criterion 6
 * 1) M Phase
 * 2) Spindle pole
 * 3) Mitosis
 * 4) M Phase of Mitotic Cell Cycle
 * 5) Spindle
 * 6) Cell Cycle Phase
 * 7) Spindle Microtubule
 * 8) Mitotic cell cycle
 * 9) Microtuble
 * 10) MIcrotuble cytoskeleton

Criterion 7
 * 1) Startle response
 * 2) Glycine gated chloride channel activity
 * 3) Transmembrane receptor activity
 * 4) Synapse part
 * 5) Glycine binding
 * 6) Glycine gated ion channel activity
 * 7) Postsynaptic membrane
 * 8) Immune response
 * 9) Immunse system process
 * 10) Receptor activity

Excel Files
[[Media:IncHvsPgFold-Criterion0 FILTERED.xls|Increased H VS PG FOLD]]

[[Media:DecHvsPgFold-Criterion1-GO.xls|Decreased H VS PG FOLD]]

[[Media:IncMetvsPGFoldCriterion2-GO_FILTERED.xls|Increased MET VS PG FOLD]]

[[Media:DecMetvsPGFold-Criterion3-GO FILTERED.xls|Decreased MET VS PG FOLD]]

[[Media:IncHvsMetFold-Criterion4-GO_FILTERED.xls|Increased H VS MET FOLD]]

[[Media:DecHvsMetFold-Criterion5-GO_FILTERED.xls|Decreased H VS MET FOLD]]

[[Media:IncAIvsPGFOLD-Criterion6-GO_ICNREAED.xls|Increased AI VS PG FOLD]]

[[Media:DecAIvsPGfold-Criterion7-GO_INCREAED.xls|Decreased AI VS PG FOLD]]

Interpretations
To best understand this data I decided to look at the filtered results and define what they meant through the Gene Ontology.

Increase H vs PG

 * Neutrophil Chemotaxis:The directed movement of a neutrophil cell, the most numerous polymorphonuclear leukocyte found in the blood, in response to an external stimulus, usually an infection or wounding.
 * Leukocyte chemotaxis: The movement of a leukocyte in response to an external stimulus
 * Activation of MAPK activity: The initiation of the activity of the inactive enzyme MAP kinase by phosphorylation by a MAPKK.
 * Positive regulation of MAPK activity: See above
 * Leukocyte migration: The movement of a leukocyte within or between different tissues and organs of the body.
 * Metanephros development: The process whose specific outcome is the progression of the metanephros over time, from its formation to the mature structure. In mammals, the metanephros is the excretory organ of the fetus, which develops into the mature kidney and is formed from the rear portion of the nephrogenic cord. The metanephros is an endocrine and metabolic organ that filters the blood and excretes the end products of body metabolism in the form of urine.
 * Kidney Development: See above
 * Uteteric bud development:The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure.
 * Viral genome replication: Any process involved directly in viral genome replication, including viral nucleotide metabolism.
 * Positive Regulation of transport: Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells by means of some external agent such as a transporter or pore.
 * Neuron apoptosis: The process of apoptosis in neurons, the basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system.
 * Immune response activating signal transduction: The cascade of processes by which a signal interacts with a receptor, causing a change in the level or activity of a second messenger or other downstream target, and ultimately leading to activation or perpetuation of an immune response.

Decrease H vs PG
Deals with decreases in Nucleosome activity, Chromatin activity, Chromosomal activity, DNA packaging, Lyase activity


 * Nucleosome: A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
 * Chromatin assembly: The assembly of DNA, histone proteins, and other associated proteins into chromatin structure, beginning with the formation of the basic unit, the nucleosome, followed by organization of the nucleosomes into higher order structures, ultimately giving rise to a complex organization of specific domains within the nucleus.
 * Chromosomal part: Any constituent part of a chromosome, a structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
 * DNA packaging: Any process by which DNA and associated proteins are formed into a compact, orderly structure.
 * Fatty acid biosynthetic process: The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
 * Lyase activity: Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

Increase Met vs PG
Shows increases in Mitosis, spindle organization, Chromosome segregation, DNA replication.
 * Mitosis: A cell cycle process comprising the steps by which the nucleus of a eukaryotic cell divides; the process involves condensation of chromosomal DNA into a highly compacted form. Canonically, mitosis produces two daughter nuclei whose chromosome complement is identical to that of the mother cell.
 * M phase of mitotic cell cycle: A cell cycle process comprising the steps by which a cell progresses through M phase, the part of the mitotic cell cycle during which mitosis takes place.
 * Spindle organization and biogenesis: A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
 * Sister chromatid segregation: The process by which sister chromatids are organized and then physically separated and apportioned to two or more sets.
 * Chromosome segregation: The process by which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets.
 * DNA replication initiation: The process by which DNA replication is started; this involves the separation of a stretch of the DNA double helix, the recruitment of DNA polymerases and the initiation of polymerase action.

Decrease Met vs PG

 * Muscle contraction: A process whereby force is generated within muscle tissue, resulting in a change in muscle geometry. Force generation involves a chemo-mechanical energy conversion step that is carried out by the actin/myosin complex activity, which generates force through ATP hydrolysis.
 * Chromatin remodeling complex: Any complex that mediates dynamic changes in eukaryotic chromatin.
 * Oxidoreductase activity: Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
 * Myelination: The process by which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.

Powerpoint
[[Media:DNABioinformaticsFINAL.ppt|Powerpoint]]