Janelle N. Ruiz Assignment 13

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.

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
 * Color coding:

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
 * 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
[[Media:IncHvsPgFold-Criterion0 FILTERED.xls|Increased 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]]