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

BMC Genomics

Table 2 Genes validated for differential expression

Gene ID	Gene Name	Description	FCM	FCV
29765	TMOD4	tropomodulin 4 (muscle)	-1564	-3065*
270	AMPD1	adenosine monophosphate deaminase 1 (isoform M)	-1320	-2799*
4604	MYBPC1	myosin binding protein C, slow type	-1128	-1574*
58529	MYOZ1	myozenin 1	-546.7	-3449*
5837	PYGM	phosphorylase, glycogen; muscle	-277.4	-3444**
4618	MYF6	myogenic factor 6 (herculin)	-265.7	-258.8*
129446	XIRP2	xin actin-binding repeat containing 2	-216.1	-498.5*
825	CAPN3	calpain 3, (p94)	-164.2	-497.9*
1375	CPT1B	carnitine palmitoyltransferase 1B (muscle)	-151.4	-109.5*
7352	UCP3	uncoupling protein 3 (mitochondrial, proton carrier)	-106.5	-2086**
55303	GIMAP4	GTPase, IMAP family member 4	-71.28	-146.3*
7070	THY1	Thy-1 cell surface antigen	+16.67	+18.15*
151887	CCDC80	coiled-coil domain containing 80	+31.02/17.06^D	+7.04*
3091	HIF1A	hypoxia-inducible factor 1, alpha subunit	+34.89	+19.62*
7153	TOP2A	topoisomerase (DNA) II alpha 170kDa	+43.58	+5.83*
1026	CDKN1A	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	+192.8	+31.67*
57214	KIAA1199	KIAA1199	+1279	+370.6*

List of genes with changed expression as validated by RT and real-time PCR (PYGM, UCP3, THY1) or QuantiGene Plex (the remaining genes). For each targeted gene, the expression was determined relative to the B2M (in RT and real-time PCR) or TFRC (in QuantiGene Plex) genes. Similar data were obtained with QuantiGene Plex when the B2M gene was used as a control (data not shown). For each gene, the fold change in gene expression was calculated between mean values in cultured myotubes versus SM biopsy. The significance of differences was estimated by a paired t-test: *p < 0.01 and **p < 0.005. The first, second and third columns are as in Table 1, the fourth lists the fold change in the microarray (FCM) as in Table 1 and the fifth the fold change in the validation techniques (FCV), with a negative symbol for downregulated genes and a positive symbol for upregulated genes. The Pearson correlation coefficient between FCM and FCV values is 0.684 (including the two copies of the CCDC80 gene).

ISSN: 1471-2164