Table 3 Annotation enrichments of PPI proteins.

From: Using machine learning to predict protein–protein interactions between a zombie ant fungus and its carpenter ant host

Test proteins (n)

GO

PFAM

WGCNA

Ophiocordyceps (129)

0

1

3

 After shared PPIs removed (125)

1

1

3

 After shared host proteins removed (26)

11

0

2

Camponotus (2083)

50

74

9

 After shared PPIs removed (1901)

44

64

9

 After shared host proteins removed (147)

12

3

2

  1. We performed enrichment analyses on interspecific PPIs without homology to Ophiocordyceps self-interactions and involving upregulated, secreted Ophiocordyceps proteins and any Camponotus proteins (Fig. 1 step 5) with or without additional filtering based on shared aspecific fungal interactions (Fig. 1 step 6). We found no enrichment signal for uSSPs in the fungus. Only in the unfiltered analysis were Camponotus DEGs overrepresented—for both upregulated and downregulated genes. The number of gene co-expression modules enriched are given under column WGCNA. While typically more stringent filtering reduced the number of enrichments detected, it increased the number of enriched GO terms for Ophiocordyceps. These enrichments included oxidation–reduction terms and various general binding terms (e.g., “binding,” “catalytic activity,” “cofactor binding,” or “ion binding”).
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