Janelle N. Ruiz Assignment 13: Difference between revisions

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==Excel Files==
==Filtered Excel Files==


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

Revision as of 11:43, 20 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.

Our 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.

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


Filtered 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

Janelle N. Ruiz

Class Links

BIOL 398.01/Spring 2010

Journal Assignments

Janelle N. Ruiz Assignment 2 Janelle N. Ruiz Assignment 5 Janelle N. Ruiz Assignment 8 Janelle N. Ruiz Assignment 12 Janelle N. Ruiz Assignment 14
Janelle N. Ruiz Assignment 3 Janelle N. Ruiz Assignment 6 Janelle N. Ruiz Assignment 9 Janelle N. Ruiz Assignment 13 Janelle N. Ruiz Assignment 15
Janelle N. Ruiz Assignment 4 Janelle N. Ruiz Assignment 7 Janelle N. Ruiz Assignment 11
  • Shared Journal
  1. BIOL398-01/S10:Class Journal Week 2
  2. BIOL398-01/S10:Class Journal Week 3
  3. BIOL398-01/S10:Class Journal Week 4
  4. BIOL398-01/S10:Class Journal Week 5
  5. BIOL398-01/S10:Class Journal Week 6
  6. BIOL398-01/S10:Class Journal Week 7
  7. BIOL398-01/S10:Class Journal Week 8
  8. BIOL398-01/S10:Class Journal Week 9
  9. BIOL398-01/S10:Class Journal Week 11
  10. BIOL398-01/S10:Class Journal Week 12
  11. BIOL398-01/S10:Class Journal Week 13
  • Assignments
  1. BIOL398-01/S10:Week 2
  2. BIOL398-01/S10:Week 3
  3. BIOL398-01/S10:Week 4
  4. BIOL398-01/S10:Week 5
  5. BIOL398-01/S10:Week 6
  6. BIOL398-01/S10:Week 7
  7. BIOL398-01/S10:Week 8
  8. BIOL398-01/S10:Week 9
  9. BIOL398-01/S10:Week 11
  10. BIOL398-01/S10:Week 12
  11. BIOL398-01/S10:Week 13
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