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Table 4 Statistics on edges from inferred SysGenSIM networks

From: Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation

  K 1.5 K 2 K 2.5
Inference algorithm Edges TPs FPs Edges TPs FPs Edges TPs FPs
PGnew 14353 6239 8114 20477 7422 13055 27496 8258 19239
PGnew + TRANSWESDu,w, -15.60% -0.57% -27.16% -15.71% -1.96% -23.52% -14.89% -3.48% -19.79%
PGnew + TRANSWESDs,w, -15.35% -0.40% -26.83% -15.17% -1.60% -22.89% -14.44% -3.04% -19.34%
PGnew + TRANSWESDu,w,2 -37.47% -16.01% -53.97% -42.82% -25.03% -52.93% -46.69% -33.13% -52.51%
PGnew + TRANSWESDs,w,2 -37.24% -15.65% -53.85% -42.38% -24.17% -52.73% -46.09% -31.77% -52.23%
PGnew + LTRu,u -32.06% -9.68% -49.27% -35.28% -15.07% -46.77% -37.67% -19.83% -45.33%
PGnew + LTRs,u -31.93% -9.51% -49.17% -35.03% -14.61% -46.64% -37.36% -19.20% -45.16%
PGnew + LTRu,w -29.74% -5.76% -48.18% -30.64% -7.79% -43.63% -28.62% -8.87% -37.10%
PGnew + LTRS,W -29.64% -5.66% -48.09% -30.49% -7.53% -43.54% -28.45% -8.53% -37.00%
  1. The number of edges in the perturbation graph and the number of FPs and TPs are shown in the table. The relative reduction of these measures (edges, TPs and FPs) in the graphs obtained after applying the different TR techniques compared to the PG is also displayed. These averaged statistics are computed from the analysis of the graphs obtained after inferring the 30 SysGenSIM networks simulated according to noise configuration 1 (LL; see Table 2). Thresholds used are β = 2.0 and γ = 0.05 for generating PGnew, α = 0.95 for TRANSWESD·,w,, α = 1.50 for TRANSWESD·,w,2 and α = 0.15 for LTR·,w. Analogous tables for the other 8 noise configurations (2, …, 9) are shown in Tables T3–T10 in Additional file 1.