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. Increased HvsPGfold >.25 AND HvsPGTtest <.05 Decreased HvsPGfold <-.25 AND HvsPGTtest <.05 Increased MetvsPGTest >.25 AND MetvsPG

Increased colors HvsPGfold inc=Red Opposite decreased Green MetvsPGfold inc=Brown Opposite decrease light blue HvsMetfold inc=Orange Opposite decreased light green AlVsPGfold inc=Purple Opposite blue

Grey no criteria

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

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