Supplementary Table 3: List of gene sets positively or negatively enriched during macrophages stimulation obtained with GSEA approach.

Name of the compared set / our set / original set / ES / NES / Nominal p-value / Brief description of the gene set / Source publication
SANA_TNFA_ENDOTHELIAL_UP / 32 / 84 / 0.8209 / 2.7593 / 0.0000 / Genes up-regulated by TNFA in colon,derm,iliac,aortic,lung endothelial cells / Pubmed 15749026
TAKEDA_NUP8_HOXA9_10D_UP / 59 / 190 / 0.6538 / 2.5128 / 0.0000 / Effect of NUP98-HOXA9 on gene transcription at 10 d after transduction UP / Pubmed 16818636
TAKEDA_NUP8_HOXA9_8D_UP / 55 / 151 / 0.6632 / 2.5112 / 0.0000 / Effect of NUP98-HOXA9 on gene transcription at 8 d after transduction UP / Pubmed 16818636
REOVIRUS_HEK293_UP / 68 / 237 / 0.6076 / 2.4400 / 0.0000 / Up-regulated at any timepoint up to 24 hours following infection of HEK293 cells with reovirus strain T3Abney / Pubmed 12885910
LINDSTEDT_DEND_8H_VS_48H_UP / 25 / 67 / 0.7666 / 2.4283 / 0.0000 / Genes up-regulated in DC stimulated for 8 h as compared to DC stimulated for 48 h / Pubmed 12356685
BENNETT_SLE_UP / 16 / 31 / 0.8593 / 2.4262 / 0.0000 / Genes Significantly up-regulated in SLE patient Blood Mononuclear Cells / Pubmed 12642603
IFNA_HCMV_6HRS_UP / 20 / 53 / 0.8106 / 2.4251 / 0.0000 / Up-regulated in fibroblasts at 6 hours following treatment with interferon-alpha / Pubmed 11711622
DAC_BLADDER_UP / 16 / 29 / 0.8439 / 2.4062 / 0.0000 / Upregulated by DAC treatment in T24 bladder carcinoma cells / Pubmed 11861364
TAKEDA_NUP8_HOXA9_3D_UP / 83 / 187 / 0.5821 / 2.4029 / 0.0000 / Effect of NUP98-HOXA9 on gene transcription at 3 d after transduction UP / Pubmed 16818636
CMV_HCMV_TIMECOURSE_12HRS_UP / 16 / 26 / 0.8502 / 2.4026 / 0.0000 / Up-regulated in fibroblasts following infection with human cytomegalovirus, with maximum change at 12 hours / Pubmed 11711622
CMV_8HRS_UP / 17 / 32 / 0.8310 / 2.3778 / 0.0000 / Upregulated at 8hrs following infection of primary human foreskin fibroblasts with CMV / Pubmed 9826724
SANA_IFNG_ENDOTHELIAL_UP / 32 / 76 / 0.6841 / 2.3472 / 0.0000 / Genes up-regulated by interferon-gamma in colon,derm,iliac,aortic,lung endothelial cells / Pubmed 15749026
CMV-UV_HCMV_6HRS_UP / 47 / 121 / 0.6243 / 2.3014 / 0.0000 / Up-regulated in fibroblasts at 6 hours following infection with UV-inactivated human cytomegalovirus / Pubmed 11711622
GALINDO_ACT_UP / 43 / 88 / 0.6374 / 2.3003 / 0.0000 / Most significant genes up-regulated by Act in macrophages from 0 to 2 h as determined by four separate analysis methods / Pubmed 12824169
RADAEVA_IFNA_UP / 25 / 52 / 0.7269 / 2.2966 / 0.0000 / Genes up-regulated by interferon-alpha in primary hepatocyte / Pubmed 11910354
TAKEDA_NUP8_HOXA9_16D_UP / 43 / 172 / 0.6336 / 2.2728 / 0.0000 / Effect of NUP98-HOXA9 on gene transcription at 16 d after transduction UP / Pubmed 16818636
IFN_BETA_UP / 32 / 65 / 0.6733 / 2.2606 / 0.0000 / Upregulated 2-fold in HT1080 cells 6 hours following treatment with interferon beta / Pubmed 9861020
IFNALPHA_NL_UP / 15 / 27 / 0.8199 / 2.2604 / 0.0000 / Upregulated by interferon alpha treatment in normal primary hepatocytes / Pubmed 11910354
IFN_ANY_UP / 38 / 82 / 0.6422 / 2.2581 / 0.0000 / Upregulated 2-fold in HT1080 cells 6 hours following treatment with any of interferons alpha, beta and gamma / Pubmed 9861020
DER_IFNA_UP / 37 / 67 / 0.6346 / 2.2312 / 0.0000 / Genes up-regulated by interferon-alpha in HT1080 (fibrosarcoma) / Pubmed 9861020
GPCRDB_OTHER / 19 / 71 / -0.4916 / -1.4952 / 0.0344 / NA / NA
AGED_MOUSE_HYPOTH_DN / 23 / 38 / -0.4597 / -1.4996 / 0.0444 / Down-regulated in the hypothalamus of aged (22 months) BALB/c mice, compared to young (2 months) controls / Pubmed 11172053
HSA05211_RENAL_CELL_CARCINOMA / 31 / 69 / -0.4247 / -1.5032 / 0.0317 / Genes involved in renal cell carcinoma / Pubmed 18077471
INNEREAR_UP / 25 / 41 / -0.4491 / -1.5033 / 0.0449 / Genes prefentially expressed in human inner ear tissue (cochlea and vestibule), at least 10-fold higher from a mixture of 29 other tissues / Pubmed 11888886
HSA03320_PPAR_SIGNALING_PATHWAY / 37 / 70 / -0.4133 / -1.5221 / 0.0182 / Genes involved in PPAR signaling pathway / Pubmed 18077471
HSA05130_PATHOGENIC_ESCHERICHIA_COLI_INFECTION_EHEC / 17 / 53 / -0.4979 / -1.5304 / 0.0493 / Genes involved in pathogenic Escherichia coli infection - EHEC / Pubmed 18077471
STRIATED_MUSCLE_CONTRACTION / 22 / 39 / -0.4693 / -1.5448 / 0.0432 / NA / NA
NADLER_OBESITY_UP / 36 / 59 / -0.4254 / -1.5582 / 0.0191 / Genes with increased expression with obesity / Pubmed 11027337
UVB_NHEK1_UP / 84 / 177 / -0.3597 / -1.5672 / 0.0118 / Upregulated by UV-B light in normal human epidermal keratinocytes / Pubmed 12771951
PEPTIDE_GPCRS / 29 / 75 / -0.4367 / -1.5690 / 0.0216 / NA / NA
SANSOM_APC_LOSS5_UP / 22 / 93 / -0.4996 / -1.5783 / 0.0371 / The top 100 genes upregulated following Apc loss at day 5 (day4) / Pubmed 15198980
HSA04150_MTOR_SIGNALING_PATHWAY / 19 / 48 / -0.5148 / -1.5823 / 0.0306 / Genes involved in mTOR signaling pathway / Pubmed 18077471
HSA03010_RIBOSOME / 46 / 98 / -0.4251 / -1.6251 / 0.0137 / Genes involved in ribosome / Pubmed 18077471
BRCA1_MES_UP / 19 / 40 / -0.5381 / -1.6793 / 0.0195 / Genes with reduced expression in mouse embryonic stem cells with a targeted deletion of BRCA1, whose expression was rescued by ectopic expression of a BRCA1 transgene / Pubmed 11384963
APPEL_IMATINIB_UP / 20 / 33 / -0.5516 / -1.7486 / 0.0084 / Genes up-regulated by imatinib during dendritic cell differentiation / Pubmed 15756019
SIG_REGULATION_OF_THE_ACTIN_ CYTOSKELETON_BY_RHO_GTPASES / 17 / 35 / -0.6245 / -1.8553 / 0.0022 / Genes related to regulation of the actin cytoskeleton / NA
BRENTANI_CYTOSKELETON / 15 / 25 / -0.6415 / -1.9199 / 0.0064 / Cancer related genes also related to the cytoskeleton / Pubmed 14593198
RIBOSOMAL_PROTEINS / 65 / 123 / -0.4677 / -1.9654 / 0.0 / NA / NA