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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
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BMC Genomics

ISSN: 1471-2164

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