Janelle N. Ruiz Assignment 13: Difference between revisions

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==Excel Files==
==Running GenMAPP==
'''Our number of errors was 1792'''
 
*We labeled our data in 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
etc.
 
*Color coding:
Increased H VS PG FOLD: Red
Decreased H VS PG FOLD: Green
Increased MET VS PG FOLD: Brown
Decreased MET VS PG FOLD: Light Blue
Increased H VS MET FOLD: Orange
Decreased H VS MET FOLD: Light Green
Increased AI VS PG FOLD: Pink
Decreased AI VS PG FOLD: Blue
No criteria: grey
 
We 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'''
#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
 
 
 
==Filtered Excel Files==


[[Media:IncHvsPgFold-Criterion0 FILTERED.xls|Increased H VS PG FOLD]]
[[Media:IncHvsPgFold-Criterion0 FILTERED.xls|Increased H VS PG FOLD]]
[[Media:DecHvsPgFold-Criterion1-GO.xl|Decreased 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]]
 
==Powerpoint==
 
[[Media:DNABioinformaticsFINAL.ppt|Powerpoint]]
 
{{Janelle N. Ruiz}}

Latest revision as of 17:20, 25 April 2010

Running GenMAPP

Our number of errors was 1792

  • We labeled our data in 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 etc.

  • Color coding:

Increased H VS PG FOLD: Red Decreased H VS PG FOLD: Green Increased MET VS PG FOLD: Brown Decreased MET VS PG FOLD: Light Blue Increased H VS MET FOLD: Orange Decreased H VS MET FOLD: Light Green Increased AI VS PG FOLD: Pink Decreased AI VS PG FOLD: Blue No criteria: grey

We 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

Powerpoint

Powerpoint

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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