Table 5.

The most significantly enriched GO terms for molecular biological process for the predicted targets of the differentially expressed miRNAs following Smad4 reexpression

GO term	Cluster frequency (out of 30,854 genes)	Genome frequency of use (out of 51,743 genes)	P-value	Corrected P-value
cellular process	21,945 (71.1%)	34,615 (66.9%)	2.03e−135	3.46e−133
single-organism process	16,897 (54.8%)	26,171 (50.6%)	6.57e−119	1.11e−116
developmental process	4,416 (14.3%)	6,062 (11.7%)	2.07e−115	3.52e−113
single-organism cellular process	13,739 (44.5%)	21,184 (40.9%)	2.93e−91	4.98e−89
metabolic process	15,628 (50.7%)	24,384 (47.1%)	2.19e−85	3.72e−83
biosynthetic process	7,285 (23.6%)	10,771 (20.8%)	1.50e−82	2.56e−80
cellular metabolic process	13,537 (43.9%)	20,960 (40.5%)	7.92e−81	1.34e−78
anatomical structure development	3,194 (10.4%)	4,389 (8.5%)	1.82e−80	3.10e−78
cellular component organization	5,065 (16.4%)	7,347 (14.2%)	4.72e−71	8.02e−69
cellular component organization or biogenesis	5,107 (16.6%)	7,419 (14.3%)	2.80e−70	4.76e−68
cellular nitrogen compound metabolic process	8,866 (28.7%)	13,540 (26.2%)	1.38e−59	2.35e−57
nitrogen compound metabolic process	9,067 (29.4%)	13,871 (26.8%)	3.37e−59	5.74e−57
cell differentiation	1,839 (6.0%)	2,476 (4.8%)	2.66e−55	4.53e−53
single-organism developmental process	2,283 (7.4%)	3,161 (6.1%)	1.61e−52	2.75e−50
Localization	7,104 (23.0%)	10,785)20.8%)	8.54e−51	1.45e−48
organelle organization	1,865 (6.0%)	2,574 (5.0%)	3.28e−44	5.58e−42
cell–cell signaling	1,117 (3.6%)	1,475 (2.9%)	6.47e−40	1.10e−37
cellular developmental process	1,993 (6.5%)	2,803 (5.4%)	1.02e−38	1.73e−36
cell communication	8,167 (26.5%)	12,684 (24.5%)	7.68e−37	1.30e−34
signaling	8,167 (26.5%)	12,684 (24.5%)	7.68e−37	1.30e−34
single organism signaling	8,167 (26.5%)	12,684 (24.5%)	7.68e−37	1.30e−34
biological regulation	8,400 (27.2%)	13,094 (25.3%)	8.48e−35	1.44e−32

Note: Terms from the process ontology with P-value as good or better than 1.

Abbreviation: GO, Gene Ontology.