Arabidopsis Example

This is a study on the response of Arabidopsis leaves to treatment with Indol Acetic Acid at two different levels (HighIAA, and LowIAA). The dataset has two series and 2 time-points. (1 and 3 hours), plus the 0 time-point.

Data: arabidopsis_data.txt
Covariates:arabidopsis_cov.txt

ASCA-genes

Variability associated to each factor:

  • Time 19.92 %
  • Treatment+TimexTreatment 19.76 %
  • Residuals 60.32 %

Variability explained for each submodel :

  • With 1 component, Submodel Time explains 64.27% of variation of factor Time.
  • With 1 component, Submodel Treatment+TimexTreatment explains 67.76% of variation of factor Treatment+TimexTreatment.

Trajectory plot of time submodel:
Time
Trajectory plot of Treatment+TimexTreatment submodel:
Treatment+TimexTreatment

ASCA-Functional


By applying ASCA-Functional to the first component of the second submodel 78 functional categories are selected by choosing a significant level of 0.05 in the GSA anlaysis and GO Biological Procceses annotations.

maSigPro

By applying maSigPro with degree=2, R-squared=0.7 and alpha=0.05 we obtained as significant:

  • 590 genes with changes in Low-IAA trajectory.
  • 549 genes with differences between High-IAA and Low-IAA trajectories.

As the most interesting genes are those with differences between both groups we represent in 9 groups the trajectories of the second gene-selection (549 genes). In the following plot red colour represent the trend of Low-IAA group and green the High-IAA.
Clusters

examples.arabidopsis.txt · Last modified: 2010/05/05 12:25 by mjnueda
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