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Red lines represent values computed using our model.
In panels (a) and (b), solid lines represent values computed using our model.
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For the CV setup, numbers represent average values computed across the training and test folds (5-fold CV) F, P and C represent molecular function, biological process and cellular component, respectively.
For the CV setup, numbers represent average values computed across the training and test folds (5-fold CV) To perform a fair comparison across setups we first identified the GO subgraph that consists of only the GO categories common to all three setups (CV, NA and NP).
In Figure 2 figure supplement 2D, the same method was used on lowly, medium, and highly expressed genes without scaling between 0 and 1 but instead dividing by the binding values of Pol II. Figure 2 figure supplement 2C represents mean values computed as mentioned above using only one region −/+500 bp around TSSs without removing outliers and scaling.
The solid lines represent the mean values computed in the ground truth in the normal (red) and lesioned (yellow) tissues.
Data represent values of three separate experiments.
Additive information values (Code(x) + Code y) in Fig. 2B) represent the sum of information values computed for each pattern of neural responses separately, with separate extrapolation to infinite dataset size.
The boxplots of Figure 2E represent two sets of mean values computed on: the antisense region which was defined as covering 500 bp before TSS and the sense region as covering 500 bp after.
Relative expression profiles for 454-sequencing were represented by Relative Abundance (RA) values computed as the absolute sample sequence count divided by the total sequence count in that sample.
Values on column plots represent –log10 binomial p-value), computed using GREAT with the default association rules.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com