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]] | ||
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[[Media:DecHvsMetFold-Criterion5-GO_FILTERED.xls|Decreased 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.
- 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
Filtered Excel Files
Powerpoint
Class Links
Journal Assignments
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- BIOL398-01/S10:Class Journal Week 2
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