Table 3. Top 10 biological processes, as determined by sub-network enrichment analysis, associated with genes in rough lemon that were significantly (P<0.05) upregulated or downregulated in response to CLas infection.

Ontology	Gene name	P-value
Upregulated biological processes
Defense response	RBOHD, MPK3, SOBIR1, WRKY70, RHL41, ATAF1, ERF-1, WRKY33, JAZ1, BAP2, WRKY40, STZ,BT1	1.77E−06
Biotic stress trait	ERF-1, WRKY33, MKK9, WRKY40, STZ	1.30E−05
Plant defense	RBOHD, MPK3, SOBIR1, WRKY70, ERF-1, NAC062, WRKY33, MKK9, WRKY40, STZ	3.15E−05
Plant immunity	MPK3, SOBIR1, ATAF1, ERF-1, NAC062, WRKY40	5.92E−05
Leaf senescence	SAUL1, WRKY70, ATAF1, JAZ8, MKK9, RAP2.4	4.41E−04
Jasmonate response	WRKY70, ERF-1, JAZ1, CML37	5.24E−04
Stomatal movement	RBOHD, MPK3, NCED3, CYP707A1, WRKY70, ATAF1, ERF-1, WRKY46	5.30−04
Jasmonate metabolism	WRKY70, ERF-1	6.75E−04
Response to ethylene stimulus	MPK3, ACS6, ERF-1, MKK9, RAP2.4	7.33E−04
Abiotic stress	MPK3, RHL41, ATAF1, NAC062, WRKY33, STZ	8.21E−04
Downregulated biological processes
Root phototropism	NPH4, PKS1	7.59E−05
Seed width	NPH4, ARF8	1.16E−04
Cell expansion	ERS1, CKI1, NPH4, ARF8, TUB1	1.33E−04
Hypocotyl growth	CYP83B1, NPH4, PIL1, ARF8, PKS1	1.88E−04
Hypocotyl shape	NPH4, PKS1	4.81E−04
Flower development	ERS1, SEX1, DME, PIL1, ARF8, LUH	1.81E−03
Fruit set	NPH4, ARF8	2.59E−03
Shade avoidance	CYP83B1, PIL1	2.69E−03
Response to ethylene stimulus	ERS1, NPH4, EBF1	3.17E−03
De-etiolation	CYP83B1, PIL1	3.92E−03