Comparative gene expression profiling between human cultured myotubes and skeletal muscle tissue

BMC Genomics

Table 3 Significantly regulated canonical pathways

	Score	Ratio	Number of Focus Genes
Signaling Pathways
Mitochondrial Dysfunction	7.88	17.60%	30
Integrin Signaling	3.52	14.50%	28
Hepatic Fibrosis/Hepatic Stellate Cell Activation	2.38	14.10%	19
Caveolar-mediated Endocytosis	2.02	14.80%	12
Regulation of Actin-based Motility by Rho	1.77	13.00%	12
Actin Cytoskeleton Signaling	1.46	10.40%	23
Apoptosis Signaling	1.35	12.10%	11
Circadian Rhythm Signaling	1.31	15.60%	5
p53 Signaling	1.29	12.60%	11
PTEN Signaling	1.29	11.70%	11
Metabolic Pathways
Citrate Cycle	6.27	20.30%	12
Oxidative Phosphorylation	4.61	15.90%	25
Ubiquinone Biosynthesis	3.66	12.50%	13
Glycolysis/Gluconeogenesis	3.39	12.10%	17
Pyruvate Metabolism	3.15	9.66%	14
Tyrosine Metabolism	3.01	6.45%	12
Butanoate Metabolism	2.61	8.53%	11
One Carbon Pool by Folate	2.51	15.80%	6
Glycosaminoglycan Degradation	1.85	9.84%	6
Biosynthesis of Steroids	1.78	4.72%	6
Alanine and Aspartate Metabolism	1.67	9.30%	8
Propanoate Metabolism	1.54	7.14%	9
Lysine Degradation	1.34	6.25%	9

Canonical pathways that have significant associations with the whole set of regulated transcripts were assessed using IPA software. The scores are shown as -log(p-value) in order to show positive numbers. The p-value was calculated by IPA using Fisher's Exact Test. A threshold value of 1.3 was selected (p-value < 0.05). The first column lists the signaling or metabolic pathways; the second the score value; the third the ratio, which represents the proportion of genes from the dataset over the total number of genes in the pathway; and the fourth the number of focus genes.

ISSN: 1471-2164