Table 3.
Top 20 curated enriched gene sets in circulating lymphocytes and monocytes of each group comparison by GSEA (p < 0.05, FDR q-value < 0.05 and FWER p-value < 0.05).
| T2DMpoorly-DL-P vs Healthy | |||||||
|---|---|---|---|---|---|---|---|
| GS follow link to MSigDB | SIZE | ES | NES | NOM p-val | FDR q-val | FWER p-val | |
| 1 | JISON_SICKLE_CELL_DISEASE_UP | 177 | −1 | −2.36 | 0 | 0 | 0 |
| 2 | RAGHAVACHARI_PLATELET_SPECIFIC_GENES | 69 | −1 | −2.27 | 0 | 0 | 0 |
| 3 | REACTOME_ANTIMICROBIAL_PEPTIDES | 72 | −1 | −2.19 | 0 | 0 | 0 |
| 4 | BROWNE_INTERFERON_RESPONSIVE_GENES | 65 | −1 | −2.17 | 0 | 0 | 0 |
| 5 | TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_UP | 180 | −1 | −2.12 | 0 | 0 | 0 |
| 6 | MOSERLE_IFNA_RESPONSE | 30 | −1 | −2.11 | 0 | 0 | 0 |
| 7 | WIERENGA_STAT5A_TARGETS_DN | 187 | −1 | −2.11 | 0 | 0 | 0 |
| 8 | HECKER_IFNB1_TARGETS | 90 | −1 | −2.11 | 0 | 0 | 0 |
| 9 | BOSCO_INTERFERON_INDUCED_ANTIVIRAL_MODULE | 73 | −1 | −2.08 | 0 | 0 | 0 |
| 10 | REACTOME_NEUTROPHIL_DEGRANULATION | 453 | −1 | −2.07 | 0 | 0 | 0 |
| 11 | TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP | 190 | −1 | −2.05 | 0 | 0 | 0 |
| 12 | TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_UP | 157 | −1 | −2.04 | 0 | 0 | 0 |
| 13 | REACTOME_DEFENSINS | 29 | −1 | −2.04 | 0 | 0 | 0 |
| 14 | BENNETT_SYSTEMIC_LUPUS_ERYTHEMATOSUS | 27 | −1 | −2.03 | 0 | 0 | 0 |
| 15 | HAHTOLA_SEZARY_SYNDROM_UP | 94 | −1 | −2.03 | 0 | 0 | 0 |
| 16 | SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP | 72 | −1 | −2.02 | 0 | 0 | 0 |
| 17 | REACTOME_INTERFERON_ALPHA_BETA_SIGNALING | 63 | −1 | −2.02 | 0 | 0 | 0 |
| 18 | SANA_RESPONSE_TO_IFNG_UP | 70 | −1 | −2 | 0 | 0 | 0 |
| 19 | TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN | 121 | −1 | −2 | 0 | 0 | 0 |
| 20 | DER_IFN_ALPHA_RESPONSE_UP | 69 | −1 | −2 | 0 | 0 | 0 |
| T2DMwell-DL-P vs Healthy | |||||||
| GS follow link to MSigDB | SIZE | ES | NES | NOM p-val | FDR q-val | FWER p-val | |
| 1 | RAGHAVACHARI_PLATELET_SPECIFIC_GENES | 69 | −1 | −2.333 | 0 | 0 | 0 |
| 2 | REACTOME_ANTIMICROBIAL_PEPTIDES | 72 | −1 | −2.16 | 0 | 0 | 0 |
| 3 | PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN | 28 | −1 | −2.018 | 0 | 0 | 0 |
| 4 | REACTOME_RESPONSE_TO_ELEVATED_PLATELET_CYTOSOLIC_CA2PLUS | 128 | −1 | −1.986 | 0 | 0 | 0 |
| 5 | COWLING_MYCN_TARGETS | 41 | −1 | −1.978 | 0 | 0 | 0 |
| 6 | JISON_SICKLE_CELL_DISEASE_UP | 177 | −1 | −1.977 | 0 | 0 | 0 |
| 7 | RICKMAN_HEAD_AND_NECK_CANCER_B | 52 | −1 | −1.909 | 0 | 0.0034737 | 0.019 |
| 8 | REACTOME_NEUTROPHIL_DEGRANULATION | 453 | −1 | −1.892 | 0 | 0.0059291 | 0.037 |
| 9 | MURATA_VIRULENCE_OF_H_PILORI | 21 | −1 | −1.886 | 0 | 0.0068948 | 0.049 |
| 10 | KAMIKUBO_MYELOID_CEBPA_NETWORK | 30 | −1 | −1.885 | 0 | 0.0063283 | 0.049 |
| DL-P vs Healthy | |||||||
| GS follow link to MSigDB | SIZE | ES | NES | NOM p-val | FDR q-val | FWER p-val | |
| 1 | RAGHAVACHARI_PLATELET_SPECIFIC_GENES | 69 | −1 | −2.394 | 0 | 0 | 0 |
| 2 | WIERENGA_STAT5A_TARGETS_DN | 187 | −1 | −2.276 | 0 | 0 | 0 |
| 3 | PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN | 28 | −1 | −2.204 | 0 | 0 | 0 |
| 4 | REACTOME_ANTIMICROBIAL_PEPTIDES | 72 | −1 | −2.166 | 0 | 0 | 0 |
| 5 | VALK_AML_CLUSTER_8 | 25 | −1 | −2.143 | 0 | 0 | 0 |
| 6 | GNATENKO_PLATELET_SIGNATURE | 42 | −1 | −2.123 | 0 | 0 | 0 |
| 7 | RICKMAN_HEAD_AND_NECK_CANCER_B | 52 | −1 | −2.108 | 0 | 0 | 0 |
| 8 | REACTOME_RUNX1_REGULATES_GENES_INVOLVED_IN_MEGAKARYOCYTE_DIFFERENTIATION_AND_PLATELET_FUNCTION | 78 | −1 | −2.06 | 0 | 3.22E-04 | 0.002 |
| 9 | HAHTOLA_SEZARY_SYNDROM_UP | 94 | −1 | −2.059 | 0 | 2.86E-04 | 0.002 |
| 10 | REACTOME_RESPONSE_TO_ELEVATED_PLATELET_CYTOSOLIC_CA2PLUS | 128 | −1 | −2.043 | 0 | 3.85E-04 | 0.003 |
| 11 | TENEDINI_MEGAKARYOCYTE_MARKERS | 61 | −1 | −2.034 | 0 | 4.68E-04 | 0.004 |
| 12 | JAATINEN_HEMATOPOIETIC_STEM_CELL_DN | 228 | −1 | −2.009 | 0 | 8.62E-04 | 0.008 |
| 13 | REACTOME_NEUTROPHIL_DEGRANULATION | 453 | −1 | −2.002 | 0 | 8.96E-04 | 0.009 |
| 14 | REACTOME_AMYLOID_FIBER_FORMATION | 89 | −1 | −1.989 | 0 | 0.0011131 | 0.011 |
| 15 | TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN | 121 | −1 | −1.988 | 0 | 0.0010389 | 0.011 |
| 16 | SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_DN | 144 | −1 | −1.985 | 0 | 9.74E-04 | 0.011 |
| 17 | VALK_AML_CLUSTER_7 | 27 | −1 | −1.977 | 0 | 0.0011464 | 0.014 |
| 18 | JISON_SICKLE_CELL_DISEASE_UP | 177 | −1 | −1.962 | 0 | 0.0017301 | 0.022 |
| Periodontitis vs Healthy | |||||||
| GS follow link to MSigDB | SIZE | ES | NES | NOM p-val | FDR q-val | FWER p-val | |
| 1 | REACTOME_INITIAL_TRIGGERING_OF_COMPLEMENT | 39 | −1 | −2.334 | 0 | 0 | 0 |
| 2 | REACTOME_CREATION_OF_C4_AND_C2_ACTIVATORS | 32 | −1 | −2.256 | 0 | 0 | 0 |
| 3 | FARMER_BREAST_CANCER_CLUSTER_1 | 45 | −1 | −2.242 | 0 | 0 | 0 |
| 4 | REACTOME_COMPLEMENT_CASCADE | 71 | −1 | −2.222 | 0 | 0 | 0 |
| 5 | REACTOME_SCAVENGING_OF_HEME_FROM_PLASMA | 30 | −1 | −2.221 | 0 | 0 | 0 |
| 6 | REACTOME_FCERI_MEDIATED_CAPLUS2_MOBILIZATION | 48 | −1 | −2.151 | 0 | 0 | 0 |
| 7 | JISON_SICKLE_CELL_DISEASE_UP | 177 | −1 | −2.136 | 0 | 0 | 0 |
| 8 | RAGHAVACHARI_PLATELET_SPECIFIC_GENES | 69 | −1 | −2.127 | 0 | 0 | 0 |
| 9 | REACTOME_ROLE_OF_LAT2_NTAL_LAB_ON_CALCIUM_MOBILIZATION | 33 | −1 | −2.116 | 0 | 0 | 0 |
| 10 | REACTOME_FCERI_MEDIATED_MAPK_ACTIVATION | 49 | −1 | −2.112 | 0 | 0 | 0 |
| 11 | REACTOME_CONDENSATION_OF_PROPHASE_CHROMOSOMES | 55 | −1 | −2.099 | 0 | 0 | 0 |
| 12 | REACTOME_REGULATION_OF_ACTIN_DYNAMICS_FOR_PHAGOCYTIC_CUP_FORMATION | 77 | −1 | −2.062 | 0 | 0 | 0 |
| 13 | REACTOME_FCGR_ACTIVATION | 30 | −1 | −2.058 | 0 | 0 | 0 |
| 14 | REACTOME_ACTIVATED_PKN1_STIMULATES_TRANSCRIPTION_OF_AR_ANDROGEN_RECEPTOR_REGULATED_GENES_KLK2_AND_KLK3 | 48 | −1 | −2.052 | 0 | 0 | 0 |
| 15 | REACTOME_AMYLOID_FIBER_FORMATION | 89 | −1 | −2.047 | 0 | 0 | 0 |
| 16 | REACTOME_HDACS_DEACETYLATE_HISTONES | 71 | −1 | −2.033 | 0 | 0 | 0 |
| 17 | WALLACE_PROSTATE_CANCER_RACE_UP | 289 | −1 | −2.024 | 0 | 0 | 0 |
| 18 | REACTOME_ROLE_OF_PHOSPHOLIPIDS_IN_PHAGOCYTOSIS | 42 | −1 | −2.02 | 0 | 0 | 0 |
| 19 | REACTOME_PRC2_METHYLATES_HISTONES_AND_DNA | 54 | −1 | −2.012 | 0 | 0 | 0 |
| 20 | REACTOME_DNA_METHYLATION | 46 | −1 | −2.012 | 0 | 0 | 0 |