Table 1 Enrichment of cassettes upstream of different gene sets.

Cassette	Experimental^a		Unchanged^b		Phagosome-associated
Cassette	Enrichment	p-value	Enrichment	p-value	Enrichment	p-value
3+5−	1.159	*7.49E−03*	0.942	7.83E−01	1.419	*3.90E−02*
3−2+	1.178	*1.98E−03*	0.978	6.15E−01	1.475	*1.90E−02*
3−6−	1.107	*3.82E−02*	0.931	8.41E−01	1.365	*4.77E−02*
5−2−	1.168	*5.22E−03*	0.958	7.12E−01	1.335	7.35E−02
6−4−	1.117	*2.71E−02*	0.946	7.79E−01	1.3	8.13E−02
8−4+	1.138	*1.08E−02*	0.953	7.49E−01	1.437	*2.49E−02*
3−2+5+	1.196	*2.73E−03*	0.978	6.02E−01	1.372	6.69E−02
3−6−4−	1.113	*3.99E−02*	0.891	9.33E−01	1.415	*4.01E−02*
6+3+5−	1.157	*1.33E−02*	0.909	8.73E−01	1.292	1.12E−01
6−4−8+	1.155	*1.01E−02*	0.947	7.56E−01	1.369	6.01E−02
3−6−4−8+	1.144	*2.15E−02*	0.888	9.22E−01	1.496	*2.89E−02*
4+6+3+5−	1.17	*1.12E−02*	0.888	9.13E−01	1.38	7.21E−02
4+6+3+5−2−	1.202	*6.25E−03*	0.897	8.76E−01	1.557	*2.98E−02*
8−4+6+3+5−	1.184	*1.04E−02*	0.849	9.59E−01	1.407	7.12E−02
4+6+3+5−2−3+	1.253	*2.09E−03*	0.943	7.19E−01	1.617	*2.72E−02*
8−4+6+3+5−2−	1.219	*5.86E−03*	0.858	9.35E−01	1.594	*3.02E−02*
1+8−4+6+3+5−2−	1.251	*7.55E−03*	0.903	8.05E−01	1.393	1.16E−01
8−4+6+3+5−2−3+	1.253	*3.56E−03*	0.897	8.42E−01	1.64	*3.00E−02*
1+8−4+6+3+5−2−3+	1.306	*3.02E−03*	0.924	7.34E−01	1.362	1.40E−01

Phagosome-associated genes are from the experimental data that were associated with the respective function or compartment based on KEGG pathways. Enrichment is calculated relative to the proportion of sequences containing at least one of the respective cassettes, relative to the control (non-discovery up-regulated) set. The p-value of the enrichment is calculated using the beta-binomial. P-values less than 0.05 are in bold. ^aExperimental dataset (non-discovery down-regulated gene sequences), ^bUnchanged dataset (sequences of genes without differential expression).

Search