Analysis 1

Objective: Differentially expressed genes in WT and KO considering the interactions between both regions (RC,HC) and treating time points(2,4,6) as replicates.

Design: Factors : Strain : WT , KO
Region : HC, RC
Interaction Terms (Contrasts) : WT-HCvsRC, KO-HCvsRC, Diff=(TRKO.RC-TRKO.HC)-(TRWT.RC-TRWT.RC)

Statistic : Moderated t-Test
Parameters Chosen:
Cutoff Value : p<0.01

Graphs: * WT vs KO:
* limm_p01_clustering.png:

Software: Limma (Bioconductor)

Analysis 2

Objective:Differentially expressed genes in HC region.

Design:

Parameters Chosen: Response Type : Two Class Pairwise Comparision
Test Statistic : t-statistic

Graphs: Up Regulated * hc_up.png:

Down Regulated * hc_down.png:

Interpretation:

Software: SAM (Bioconductor)

Analysis 3

Objective: Differentially expressed genes in RC region.

Design:

Parameters Chosen:

Graphs: * RC_UP.png:

* rc_down.png:

Interpretation:

Software: SAM (Bioconductor)

• hier_top100_mirnics.pdf:
  

Please ignore the comments included in perl scripts. I modified an already existing script written for another purpose.
I realize using OOP reduces these kinds of problems.

* Set DENYTOPICVIEW = TWikiGuest

• SET ALLOWTOPICVIEW = NeuroDeGenGroup