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:

• 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

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

Increased H VS PG FOLD

Decreased H VS PG FOLD

Increased MET VS PG FOLD

Decreased MET VS PG FOLD

Increased H VS MET FOLD

Decreased H VS MET FOLD

Increased AI VS PG FOLD

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
• 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.

Journal Assignments

KP Ramirez Week 2	KP Ramirez Week 6	KP Ramirez Week OFF
KP Ramirez Week 3	KP Ramirez Week 7	KP Ramirez Week 11
KP Ramirez Week 4	KP Ramirez Week 8	KP Ramirez Week 12
KP Ramirez Week 5	KP Ramirez Week 9	KP Ramirez Week 13

Shared Journals

1. Week 2
2. Week 3
3. Week 4
4. Week 5
5. Week 6
6. Week 7
7. Week 8
8. Week 9
9. Week 10
10. Week 11
11. Week 12
12. Week 13

Useful Links

• Introductory tutorial
• OpenWetWare help pages
• BIOL398-01/S10:People