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Table 1 Comparison of funcExplorer results with previous studies

From: funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data

Previous studies funcExplorer
      First Best F1
Dataset Organism n k C (%) k C (%) Rand(Adj.Rand) Filt. Rand(Adj.Rand) k C (%) Rand(Adj.Rand) Filt. Rand(Adj.Rand) k C (%) Rand(Adj.Rand) Filt. Rand(Adj.Rand)
CLEANsmall [21] H. sapiens 1,422 8 100% 3 100% 0.74(0.39) 0.74(0.39) 7 93.95% 0.82(0.49) 0.81(0.50) 33 58.09% 0.76(0.32) 0.91(0.76)
Arabidopsis [42] A. thaliana 4,982 8 74% 7 80.08% 0.86(0.47) 0.94(0.81) 8 79.45% 0.88(0.50) 0.96(0.86) 8 78.13% 0.88(0.50) 0.96(0.87)
Humoral [12] H. sapiens 2,579 11 46.5% 4 98.68% 0.66(0.11) 0.66(0.12) 16 81.5% 0.72(0.16) 0.74(0.22) 36 30.52% 0.55(0.10) 0.80(0.39)
Yeast [43] S. cerevisiae 1,340 6 100% 2 100% 0.52(0.07) 0.52(0.07) 21 49.85% 0.68(0.18) 0.78(0.29) 31 28.96% 0.55(0.11) 0.81(0.16)
  1. *Note: n = number of genes in the data; k = number of clusters; C (%) = gene coverage (% of genes distributed into the k clusters); Rand = Rand index (value between 0 and 1); Adj.Rand = Adjusted Rand index (corrected-for-chance version of the Rand index; value between -1 and 1); Filt. Rand/Adj.Rand = indexes calculated after excluding unclustered genes; the values used in the further comparisons are highlighted in bold; funcExplorer parameters for CLEANsmall and Humoral: p-value≤0.001; Arabidopsis: p-value≤10−7; Yeast: p-value≤0.01; no limit on term size