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1.
Figure 2

Figure 2. Plots of the fraction of BKZ or of predicted HDFs that are also differentially expressed in the AGM-PTM comparison: (a) SinkSource+ and (b) SinkSource.. From: Network-Based Prediction and Analysis of HIV Dependency Factors.

There are six plots for each algorithm, with one plot for each tissue-day combination. In each plot, the x-axis corresponds to the rank of a predicted HDF. At each rank k on the x-axis, the y-axis plots the fraction of HDFs with the top k ranks that are also differentially expressed. Note that the scale of the y-axis changes from plot to plot. The red and green curves display the results for predicted HDFs, at different prediction ranks. Red values indicate statistically significant overlaps, at the 0.05 level, between predicted HDFs and differentially-expressed genes. Green values indicate overlaps that are not statistically significant. Figures S9 and S10 plot the corresponding p-values. The horizontal dotted blue line in each plot denotes the overlap of BKZ HDFs with the corresponding set of differentially-expressed genes.

T. M. Murali, et al. PLoS Comput Biol. 2011 September;7(9):e1002164.
2.
Figure 1

Figure 1. Cross validation results on the unweighted human PPI network.. From: Network-Based Prediction and Analysis of HIV Dependency Factors.

(a) Histograms of area under precision-recall curve for all algorithm-dataset combinations. Each group of vertical bars corresponds to one algorithm. Error bars indicate one standard deviation from the mean, computed over 10 independent runs of 2-fold cross validation. Algorithm abbreviations: Hopfield (H), Local (L), SinkSource (SS), FunctionalFlow with 1 phase (FF 1), FunctionalFlow with 7 phases (FF 7), Local without negative examples (L+), SinkSource without negative examples (SS+), and PRINCE (P). Dataset abbreviations: Brass (B), Konig (K), Zhou (Z), Brass or Konig or Zhou (BKZ). (b) Precision-recall curves for the SinkSource algorithm on the four datasets. At each value of recall, error bars indicate one standard deviation in the value of precision. (c) Precision-recall curves for the SinkSource+ algorithm on the four datasets. (d) Precision-recall curves for all algorithms on the BKZ dataset.

T. M. Murali, et al. PLoS Comput Biol. 2011 September;7(9):e1002164.

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