Supplementary Table 1: Genetic network affected by genes differentially expressed in CR vs. NR
patients
ID
Molecules in network (*)
Score (†)
Focus molecule
Top functions
1
ATF2, Caspase, CCND2, CCNE2, CDKN1C, CFLAR, CyclinA, CyclinE, ERK, FAS, FMR1, GAS2, hCG, IFNbeta,
IL12, IL27RA, Interpheron alpha, LDL, MDM4, NAMPT, Nfat, PDGF BB, PI3K, PLEKHA2, Proteasome, PTPN1,
RECQL, SOAT1, STAT1, STAT5a/b, TCR, Tgf beta, WARS, XAF1, XIAP
38
19
Hematologial System Development and
Function, Immune Responser, Immune and
Lymphatic System Development and
Function
2
ACTR2, Akt, Arp2/3-F actin, ARPC1A, BCL11B, Calmodulin, CBX5, CPEB3, DYRK3, F Actin, FGD4, FSH,
GSTA4, Histone h3, IFI16, Insulin, Jnk, LNPEP, MAP6, MAP4K3, Mapk, MED13, MED31, MYO1B, NfkB,
NFYB, P38 MAPK, PLS1, PRKX, RAB3B, RNA polymerase II, SLC12A2, SYNE2, TMPO, ZNF675
33
17
Auditory disease, Cellular Growth and
Proliferation, Digestive System
Development and Function
3
AGT, ANK3, COX7A2, CTNNB1, CYP2C44, CYP3A43, CYP51A1, DDX17, DLG5, EDEM3, FASTKD2, FEM1C,
GSS, HNF4A, HOOK1, HSPA6, KLHL28, LRIG2, MGEA5, MORF4L2, PCNA, RNASE4, SIN3A, SLC39A6,
SOX17, SP1, SUDS3, TADA1L, UGCG, USP1, USP24, USP30, USP36, USP46, VEZT
33
17
Protein Degradation, Protein Sysntesis,
Cancer
4
ACAA1B,ADIG, ANKRD57, ARHGAP10, CBFA2T3, CDC42, CEP350, CPSF6, EGF, Egfr-Erbb2, RBB2, EXOC8,
EXOC6B, EZH2, GPRIN1, GTP, LIMK1, LIMK2, LRRFIP1, MPHOSPH9, PAK2, PAK6, phsphpatidylinositol-3, 45-triphsphate, PLEKHA1, PPARG, RIT1, RND3, RNF12, SGPL1, SHC1, SHCBP1, TNRC6B, UBQLN4, WSB2,
ZNF652
31
16
Cancer, Cellular Groeth and Proliferation,
Gastrintestinal Disease
5
14-3-3(), ARHGAP21, ARHGEF16, C12ORF51, C22ORF9, CLASP1, DENNC4A, EIF4A3, ERC2,
GAPVD1, GIT1, KIAA1377, KLC3, KLC4, LARP1, MAP3K5, MAPK14, MIB1, NADK,P4HA1, P4HA3, P4HB,
PFKFB2, Procollagen-proline dioxygenase, RAI14, RALGPS2, SAMD48, SH3BP5L, SPAG9, SRGAP2, YWHAA,
YWHAD, YWHAG, YWHAZ
11
7
Amino Acid Metabolism, PostTranslational Modification, Small Molecule
Biochemistry
(*) Bold genes are those identified by the microarray analysis. Other genes were either not on the expression
array or not significantly regulated. (†) A score of > 3 was considered significant (p < 0.001).
Supplementary Table 2: Representation of the distribution of the gene ontology (GO)
functions of the 157 selected probes sets. The GO classifications were sorted by the
enrichment score (ES) and the number of genes for specific function are indicated; the left
column shows the names of different functions. Some genes bear multiple functions,
1
2
cell development and differentiation
3
purine ribonucleotide binding
1,03
4
Pleckstrin-like
0,99
5
negative regulation of apoptosis
0,91
6
DNA-dependent regulation of transcription
0,90
regulation of transcription
0,87
negative regulation of transcription
0,87
induction of apoptosis
0,81
AT P binding
0,74
15 14 13 12 11 10
9
8
apoptosis and programmed cell death
7
which have all been accounted for in their different categories.
2,58
13
1,99
GT P binding
0,73
regulation of cyclin-dependent PK activity
0,65
endopeptidase activity
0,55
serine/threonine PK activity
0,50
DNA packaging
0,49
18
18
5
4
20
21
5
N. geni
4
14
4
3
3
5
5
ES