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Table 2 Pathway data sources in the functional interaction network

From: A human functional protein interaction network and its application to cancer data analysis

Data source

Proteins

SwissProt proteins (coverage)

Interactions

Reference

Reactome

4,490

3,863 (19%)

74,869

[23]

Panther

1,912

1,355 (7%)

33,425

[60]

CellMap

567

567 (3%)

1,195

[61]

NCI Nature

1,492

1,486 (7%)

10,845

[62]

NCI BioCarta

1,137

1,136 (6%)

6,695

[62]

KEGG

2,497

2,261 (11%)

13,934

[63]

TRED

1,167

1,166 (6%)

3,030

[64]

  1. SwissProt coverages were calculated as described in Table 1. NCI Pathway Interaction Database has two divisions: batch-imported pathways from BioCarta [83] and pathways hand-curated by NCI Nature pathway curators. We represent these two divisions separately. TRED is a transcription factor/target database. We have imported the human curated part of transcription factor-target interactions from this database for our network.
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Genome Biology

ISSN: 1474-760X

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