The embryonic genes Dkk3, Hoxd8, Hoxd9 and Tbx1 identify muscle types in a diet-independent and fiber-type unrelated way

Table 3 Changed gene sets in the gastrocnemius versus quadriceps.

	N	ES	NES	FDR
up-regulated cellular processes
Striated muscle contraction¹	41	0.68	2.37	0.000
Ribosome²	20	0.71	2.05	0.005
down-regulated cellular processes
Tissues, muscle, fat, bone and connective 2¹	47	-0.57	-2.14	0.003
Cell cycle¹	85	-0.52	-2.14	0.003
CTCF first multivalent nuclear factor³	17	-0.71	-2.07	0.006
Valine, leucine and isoleucine degradation²	40	-0.59	-2.16	0.006
Cell cycle G1 to S control reactome²	69	-0.49	-2.01	0.013
Antigen processing and presentation²	51	-0.52	-2.01	0.014
Mets affect on macrophage differentiation³	16	-0.69	-1.97	0.014
Amino acid metabolism¹	46	-0.52	-1.95	0.016
Porphyrin and Chlorophyll metabolism²	19	-0.64	-1.88	0.033
DNA replication reactome¹	40	-0.51	-1.86	0.038

GSEA was applied to identify up-regulated and down-regulated processes in the gastrocnemius as compared with the quadriceps in LFD mice. Presented are regulated processes with a false discovery rate (FDR) < 0.05. An FDR was calculated to adjust for multiple hypothesis testing. Sources of the gene sets: ¹GenMAPP, ²KEGG, ³Biocarta. N, number of genes; ES, enrichment score for the gene set, that reflects the degree to which a gene set is overrepresented at the top or bottom of the ranked list; FDR, NES, normalized enrichment score, that is, the normalized ES to account for the size of the set.

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