Table 6

Paralogs and network connectivity: Outdegree, indegree and betweennessa

Tetrapoda and younger

(5,495 gene set linked)

Subnetwork and overlap

Outdegree

Indegree

Betweenness

All edges (237 nodes)

3.90 [4.07, 342]

3.61 [4.07, 99]

0.41 [0.47, 266]

Positive edges only (150 nodes)

2.27 [2.15, 676]

1.98 [2.16, 262]

0.40 [0.44, 365]

Negative edges only (71 nodes)

1.70 [1.34, 905]

1.22 [1.33, 338]

0.39 [0.42, 440]

Scaffolding only (144 nodes)

3.57 [3.71, 386]

3.57 [3.70, 385]

0.43 [0.47, 369]

2ROs

(9,958 gene set linked)

Subnetwork and overlap

Outdegree

Indegree

Betweenness

All edges (1,096 nodes)

    4.34 [4.06, 999]

    4.29 [4.06, 984]

2.33 [2.19, 916]

Positive edges only (771 nodes)

2.23 [2.16, 836]

2.19 [2.16, 666]

2.40 [2.25, 879]

Negative edges only (377 nodes)

    1.48 [1.33, 996]

1.34 [1.33, 522]

    2.63 [2.30, 981]

Scaffolds only (714 nodes)

3.85 [3.72, 898]

3.85 [3.72, 885]

2.40 [2.35, 626]

Chordata

(2,173 gene set linked)

Subnetwork and overlap

Outdegree

Indegree

Betweenness

All edges (194 nodes)

4.24 [4.04, 697]

4.26 [4.06, 697]

0.44 [0.38, 792]

Positive edges only (120 nodes)

2.59 [2.14, 932]

2.31 [2.15, 707]

0.47 [0.35, 909]

Negative edges only (61 nodes)

1.55 [1.33, 789]

    1.95 [1.33, 983]

0.42 [0.36, 730]

Scaffolds only (141 nodes)

3.40 [3.70, 203]

3.40 [3.70, 216]

0.44 [0.47, 455]

Bilateria

(5,223 gene set linked)

Subnetwork and overlap

Outdegree

Indegree

Betweenness

All edges (620 nodes)

    4.87 [4.06, 1000]

    4.72 [4.05, 1000]

    1.60 [1.23, 1000]

Positive edges only (428 nodes)

    2.61 [2.16, 999]

    2.49 [2.15, 997]

    1.65 [1.24, 999]

Negative edges only (242 nodes)

    1.66 [1.33, 998]

1.49 [1.34, 903]

    1.92 [1.48, 995]

Scaffolds only (399 nodes)

    4.19 [3.73, 987]

    4.19 [3.72, 990]

1.45 [1.31, 801]


aPalogs linked with different taxons are mapped to the human cancer signalling map (HCSM). The entire network, as well as the subnetworks consisting of only positive, negative or scaffolding edges, are considered. The overlap between duplication sets of different ages and HCSM subnetworks is given in parentheses in the first column. In the remaining columns, following the value of the metric (outdegree, indegree or betweenness) calculated for the test subgraph, numbers in square brackets denote (1) the average value of the given metric calculated for 1,000 random subgraphs and (2) the number of 1,000 random subgraphs for which the given metric had lower value than for the test subgraph (the difference is significant at the P value cutoff of 0.05 if this number is lower than 50 or higher than 950, and in these cases the numbers are underlined

Huminiecki and Heldin BMC Biology 2010 8:146   doi:10.1186/1741-7007-8-146

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