KP Ramirez Week 13: Difference between revisions
Line 168: | Line 168: | ||
*'''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. | *'''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 === | ||
Revision as of 15:57, 21 April 2010
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:
- HvsPG, MetvsPG, HvsMet, and AIvsPG.
This corresponded to 8 different criteria on the Expression dataset manager.
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.
- Criterion 0 Increased H vs PG Fold
- Criterion 1Decreased H vs PG Fold
- Criterion 2 Increased Met vs PG Fold
- Criterion 3 Decreased Met vs Pg Fold
- Criterion 4 Increased H vs Met Fold
- Criterion 5 Decreased H vs Met fold
- Criterion 6 Increased AI vs PG fold
- Criterion 7 Decreased AI vs Pg fold
Top 10 Results
Criterion 0
- Regulation of retinal programmed cell death
- Neutrophil chemotaxi
- IgE binding
- Cell Surface
- Leukocye chemotaxis
- Defense response
- Peptidoglycan metabolic process
- Response to wounding
- MAPKKK Cascade
- Inflammatory response
Criterion 1
- Nucleosome
- Nucleosome assembly
- Chromatin assembly
- Chromatin assembly or dissaembly
- Cysteine biosynthetic process
- Protein carrier activity
- Protein DNA conplex assembly
- Chromatin
- Chromasomal part
- chromosome
Criterion 2
- M phase
- M phase of mitotic cell cycle
- Mitosis
- Cell Cycle phase
- Cell Division
- Mitotic Cell Cycle
- Spindle
- Cell Cycle Checkpoint
- Spindle organization and biogenesis
- Cell Cycle
Criterion 3
- Muscle contraction
- Extracellular region
- Sarcomere
- Extracellualr region part
- Contractile fiber part
- Regulation of muscle contraction
- Multicellular organismal process
- Monooxygenase activity
- Oxidoredcutase activity
- Anatomical structure development
Criterion 4
- Muscle contraction
- Multicellular organismal process
- Smooth muscle contraction
- Regulation of muscle contraction
- Anatomical structure development
- Extracellular region
- Multicellular organismal development
- Extracellular region part
- System development
- Regulation of multicellular organisms
Criterion 5
- Integral to plasma membrane
- Intrinsic to plasma membrane
- Cell communication
- Plasma membrane
- Plasma membrane part
- Signal transduction
- Receptor activity
- G-protein coupled receptor activity
- Molecular tranducer activity
- Signal transducer activity
Criterion 6
- M Phase
- Spindle pole
- Mitosis
- M Phase of Mitotic Cell Cycle
- Spindle
- Cell Cycle Phase
- Spindle Microtubule
- Mitotic cell cycle
- Microtuble
- MIcrotuble cytoskeleton
Criterion 7
- Startle response
- Glycine gated chloride channel activity
- Transmembrane receptor activity
- Synapse part
- Glycine binding
- Glycine gated ion channel activity
- Postsynaptic membrane
- Immune response
- Immunse system process
- Receptor activity
Excel Files
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
- Peptidoglycan metabolic process: The chemical reactions and pathways involving peptidoglycans, any of a class of glycoconjugates found only in bacterial cell walls and consisting of strands of glycosaminoglycan cross-linked by oligopeptides to form a huge and rigid network.
- 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.
- Myeloid leukocyte activation: A change in the morphology or behavior of a myeloid leukocyte resulting from exposure to an activating factor such as a cellular or soluble ligand
- Calcium mediated signaling: A series of molecular signals in which a cell uses calcium ions to convert an extracellular signal into a response.
- 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.
- Bone mineralization: The deposition of calcium phosphate in bone tissue.
- 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.
- Antigen receptor mediated signaling pathway: A series of molecular signals initiated by the cross-linking of an antigen receptor on a B or T cell.
- 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
Journal Assignments