Table 2.

Gene functional classification of up-regulated genes in SKF compared with those of SKP spheres (10 clusters).

Functional Cluster	Enrichment Score	Genes
Cellular protein metabolic process	4.97	ribosomal protein sa, mitochondrial ribosomal protein l13, mitochondrial ribosomal protein l23, ribosomal protein l11, mitochondrial ribosomal protein s15, ribosomal protein s5, ribosomal protein l38, mitochondrial ribosomal protein s25, ribosomal protein l24, ribosomal protein l22, ribosomal protein l27, ribosomal protein s13, mitochondrial ribosomal protein l48, mitochondrial translational initiation factor 3, mitochondrial ribosomal protein l37
Nucleotide binding	2.49	sar1 gene homolog a (s. cerevisiae), heat shock 70kda protein 8, tubulin, alpha, ubiquitous, eukaryotic translation elongation factor 1 alpha 1
Response to protein stimulus	2.14	heat shock 60kda protein 1 (chaperonin), heat shock 10kda protein 1 (chaperonin 10), heat shock 70kda protein 8, heat shock protein 90kda alpha (cytosolic), class a member 1
Cellular catabolic process	1.53	ubiquitin carboxyl-terminal esterase l1 (ubiquitin thiolesterase), proteasome (prosome, macropain) subunit, beta type, 6, proteasome (prosome, macropain) subunit, alpha type, 7, dcp1 decapping enzyme homolog a (s. cerevisiae)
Transmembrane	1.33	bmp and activin membrane-bound inhibitor homolog (xenopus laevis), solute carrier family 33 (acetyl-coa transporter), member 1, aquaporin 1 (colton blood group), tumor-associated calcium signal transducer 1
Ribonucleotide binding	1.3	dead (asp-glu-ala-asp) box polypeptide 18, heat shock 70kda protein 8, mcm8 minichromosome maintenance deficient 8 (s. cerevisiae), dead (asp-glu-ala-asp) box polypeptide 55
RNA metabolic process	1.17	heterogeneous nuclear ribonucleoprotein h3 (2h9), heterogeneous nuclear ribonucleoprotein r, rod1 regulator of differentiation 1 (s. pombe), cleavage and polyadenylation specific factor 3, 73kda
Plasma membrane	0.93	atpase, na+/k+ transporting, beta 3 polypeptide, solute carrier family 33 (acetyl-coa transporter), member 1, solute carrier family 12 (potassium/chloride transporters), member 4, solute carrier family 23 (nucleobase transporters), member 2
Protein modification	0.88	casein kinase 1, alpha 1, v-mos moloney murine sarcoma viral oncogene homolog, discoidin domain receptor family, member 1, ptk9 protein tyrosine kinase 9
Regulation of transcription	0.38	sry (sex determining region y)-box 9 (campomelic dysplasia, autosomal sex-reversal), hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor), mcm8 minichromosome maintenance deficient 8 (s. cerevisiae), taf5 rna polymerase ii, tata box binding protein (tbp)-associated factor, 100kda, nuclear factor (erythroid-derived 2)-like 1, nuclear factor (erythroid-derived 2)-like 2, pc4 and sfrs1 interacting protein 1, camp responsive element binding protein-like 2, chromosome 20 open reading frame 17, suppressor of ty 6 homolog (s. cerevisiae), rrn3 rna polymerase i transcription factor homolog (yeast), phd finger protein 23, ets homologous factor, nuclear factor of activated t-cells 5, tonicity-responsive, hypothetical protein bm-005, nuclear receptor subfamily 3, group c, member 1 (glucocorticoid receptor)