Help needed: How to interpret the output file from "X_aggregate_comparison_bound" with multiple conditions and others...

[c2b2pss]

Hi,

I am comparing the progression of 3 samples: WT >> PR >> CR in that order. Like a pseudo timeseries.

1. In the attached file "...._aggregate_comparison_bound.pdf" which compares foot prints across WT, PR, CR, but is a 4 x4 matrix of figures. How and why is this plotted this way? How do I interpret each comparison? CREB5_HUMAN.H11MO.0.D_CREB5_HUMAN.H11MO.0.D_aggregate_comparison_bound.pdf

2. In the "bindetect_results" (see example below) aggregated file how are the comparisons done, like A vs B? According to the WIki """The differential binding score for the TF between the two conditions. Negative values imply more bound in condition2""" I can conclude that more of the TF in row 1 is bound in PR than in WT?

3. Is there a fold change kind of metric that can be interppreted? How would I say "PR binds x times more than WT" or something like that?? Or is that really not possible?

Thanks!

| WT_mean_score | WT_bound | PR_mean_score | PR_bound | CR_mean_score | CR_bound | WT_PR_change | WT_PR_pvalue | PR_CR_change | PR_CR_pvalue |
|:-------------:|:--------:|:-------------:|:--------:|:-------------:|:--------:|:------------:|:------------:|:------------:|:------------:|
| 0.12317       | 9176     | 0.1576        | 12962    | 0.12729       | 10392    | -0.39182     | 4.91846E-196 | 0.26183      | 7.30073E-180 |
| 0.12048       | 9206     | 0.1542        | 12956    | 0.12466       | 10353    | -0.38908     | 1.55481E-193 | 0.26221      | 1.57677E-178 |
| 0.12065       | 9146     | 0.15503       | 12801    | 0.12446       | 10190    | -0.38507     | 8.11777E-196 | 0.2623       | 1.69253E-175 |
| 0.11889       | 9269     | 0.15139       | 12902    | 0.12237       | 10345    | -0.371       | 8.53009E-190 | 0.25516      | 3.64172E-175 |
| 0.12249       | 9165     | 0.15483       | 12726    | 0.12736       | 10384    | -0.36164     | 8.01726E-193 | 0.23559      | 6.60438E-176 |
| 0.12688       | 9777     | 0.15732       | 13264    | 0.13116       | 10980    | -0.33052     | 4.48453E-192 | 0.21647      | 1.56954E-173 |
| 0.11789       | 6394     | 0.14368       | 8370     | 0.12053       | 7177     | -0.32588     | 2.63666E-175 | 0.22962      | 3.20349E-167 |
| 0.12538       | 10090    | 0.15298       | 13428    | 0.12722       | 11098    | -0.30566     | 6.51881E-190 | 0.21202      | 2.39010E-172 |