Table 2.

Top GO biological processes enriched in each replicated module. The associated effect is shown in brackets.

ID	GO biological process	FDR
module 22 (smoking)
GO:0031333	negative regulation of protein complex assembly	1.77 × 10−02
module 11 (smoking)
GO:1901661	quinone metabolic process	6.30 × 10−06
GO:0006081	cellular aldehyde metabolic process	6.30 × 10−06
GO:0019748	secondary metabolic process	1.86 × 10−05
GO:0098869	cellular oxidant detoxification	2.05 × 10−05
GO:0034754	cellular hormone metabolic process	4.09 × 10−05
module 17 (smoking)
No significant enrichment.
module 15 (smoking)
GO:0070268	cornification	4.60 × 10−02
GO:0006486	protein glycosylation	4.60 × 10−02
GO:0043413	macromolecule glycosylation	4.60 × 10−02
GO:0016266	O-glycan processing	4.60 × 10−02
GO:0046718	viral entry into host cell	4.60 × 10−02
module 36 (sex and smoking:sex)
GO:0006413	translational initiation	1.12 × 10−03
GO:0006687	glycosphingolipid metabolic process	4.80 × 10−02
GO:0006614	SRP-dependent cotranslational protein targeting to membrane	4.80 × 10−02
GO:0006613	cotranslational protein targeting to membrane	4.80 × 10−02
GO:0045047	protein targeting to ER	4.80 × 10−02
module 02 (smoking:sex)
GO:0006914	autophagy	2.91 × 10−06
GO:0061919	process utilizing autophagic mechanism	2.91 × 10−06
GO:0000422	autophagy of mitochondrion	9.42 × 10−05
GO:0061726	mitochondrion disassembly	9.42 × 10−05
GO:0035966	response to topologically incorrect protein	4.82 × 10−04
module 34 (smoking:sex)
GO:0009615	response to virus	1.29 × 10−14
GO:0045071	negative regulation of viral genome replication	2.53 × 10−07
GO:0043900	regulation of multi-organism process	3.25 × 10−07
GO:0019079	viral genome replication	6.30 × 10−06
GO:0060337	type I interferon signaling pathway	2.52 × 10−03