Spreadsheet: 5cb76502-6350-4c1f-984b-cca566279c67
Sheet: Sheet1

Supplementary table S8: Gene Set Enrichment Analysis (GSEA) of the top hypomethylated genes in endometrial cancer. GSEA was done using a one-tailed Fisher’s exact test of the top 52 hypomethylated genes (there were 52 hypomethylated unique genes among the top ranked 500 CpGs) in endometrial cancer (compared to non-neoplastic endometrium) in Set 1 against the Molecular Signatures Database (MSigDB, Broad Institute, www.broadinstitute.org/gsea/msigdb). The columns label the gene list, the number of genes in list, the number represented on 27k array, the corresponding fraction, the number that overlap with the top 52 hypomethyated genes, the P-value of enrichment, the adjusted P-value, and the gene symbols for the enriched genes. | Unnamed: 1 | Unnamed: 2 | Unnamed: 3 | Unnamed: 4 | Unnamed: 5 | Unnamed: 6 | Unnamed: 7 | Unnamed: 8
[NAME] | nList | nRep | fRep | nOVLAP | OR | pvalue | adjPval | Genes
ZAIDI_OSTEOBLAST_TRANSCRIPTION_FACTORS | 6 | 6 | 1 | 2 | 143.478286285778 | 0.000187611597000875 | 0.527664165834895 | DLX5 MSX1
[NAME] | 35 | 34 | 0.971428571428571 | 3 | 28.4233959052544 | 0.000240904797635142 | 0.527664165834895 | FCN2 [NAME]
module_96 | 36 | 35 | 0.972222222222222 | 3 | 27.5371309319429 | 0.000262823854478221 | 0.527664165834895 | FCN2 [NAME]
PARK_APL_PATHOGENESIS_DN | 38 | 38 | 1 | 3 | 25.1805548627371 | 0.000336198895084355 | 0.527664165834895 | GAL PRTN3 CES1
PHAGOCYTOSIS | 17 | 17 | 1 | 2 | 38.3846023472507 | 0.00165855828437632 | 1 | FCN2 FCN1
NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON | 335 | 261 | 0.77910447761194 | 5 | 5.89368161084479 | 0.00237385155181953 | 1 | TMC6 CD300E CD300LB MGC15523 [NAME]
NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN | 80 | 76 | 0.95 | 3 | 12.0434523934686 | 0.00254552167822773 | 1 | BST2 MEST CES1
MESODERM_DEVELOPMENT | 22 | 22 | 1 | 2 | 28.8036157698204 | 0.00278499239958858 | 1 | MEST TRIM15
ANTIGEN_BINDING | 28 | 23 | 0.821428571428571 | 2 | 27.4363379685158 | 0.00304324780372402 | 1 | FCN2 FCN1
FARMER_BREAST_CANCER_APOCRINE_VS_BASAL | 330 | 302 | 0.915151515151515 | 5 | 5.06560229315807 | 0.00443337351199378 | 1 | FCN2 [NAME]
LENAOUR_DENDRITIC_CELL_MATURATION_DN | 100 | 95 | 0.95 | 3 | 9.54777423789021 | 0.00477814457436044 | 1 | [NAME]
SUGAR_BINDING | 34 | 32 | 0.941176470588235 | 2 | 19.1998619015367 | 0.00584456486363111 | 1 | FCN2 FCN1
AMIT_SERUM_RESPONSE_480_MCF10A | 39 | 35 | 0.897435897435897 | 2 | 17.4523257140493 | 0.00696321384587028 | 1 | [NAME]
IMMUNE_EFFECTOR_PROCESS | 38 | 37 | 0.973684210526316 | 2 | 16.442690246195 | 0.00775859445822704 | 1 | FCN2 FCN1
SABATES_COLORECTAL_ADENOMA_UP | 134 | 114 | 0.850746268656716 | 3 | 7.90168932311584 | 0.00791464515030807 | 1 | UNQ2541 SERPINB5 MSX1
GAL_LEUKEMIC_STEM_CELL_DN | 244 | 222 | 0.909836065573771 | 4 | 5.4367220288393 | 0.00816326994865192 | 1 | MS4A3 FCN1 SERPINA1 PRTN3
KRASNOSELSKAYA_ILF3_TARGETS_DN | 39 | 38 | 0.974358974358974 | 2 | 15.992610561031 | 0.00817094976729052 | 1 | GAL OLFM1
MORF_PML | 129 | 116 | 0.89922480620155 | 3 | 7.76090217280636 | 0.0083007131125861 | 1 | SSTR5 TUBGCP2 MSX1
DUNNE_TARGETS_OF_AML1_MTG8_FUSION_UP | 47 | 39 | 0.829787234042553 | 2 | 15.559874798804 | 0.0085929851258875 | 1 | MS4A3 SELPLG
WONG_ENDMETRIUM_CANCER_DN | 42 | 39 | 0.928571428571429 | 2 | 15.559874798804 | 0.0085929851258875 | 1 | [NAME]
TARTE_PLASMA_CELL_VS_PLASMABLAST_UP | 391 | 367 | 0.938618925831202 | 5 | 4.13724533368279 | 0.00992934392431121 | 1 | FCN1 KCNQ1 MSX1 SPRR1A SERPINA1
TISSUE_DEVELOPMENT | 137 | 130 | 0.948905109489051 | 3 | 6.8979553834936 | 0.0113132149323674 | 1 | SPRR1A TRIM15 MEST
FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_DN | 454 | 385 | 0.848017621145374 | 5 | 3.93636114807728 | 0.0120373465555853 | 1 | FCN1 MS4A7 KCNQ1 PARVG CES1
DOANE_BREAST_CANCER_ESR1_DN | 48 | 47 | 0.979166666666667 | 2 | 12.7857371779957 | 0.0123091887996098 | 1 | [NAME]
POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_UP | 51 | 48 | 0.941176470588235 | 2 | 12.5084665358539 | 0.0128151494966953 | 1 | SLC1A2 OLFM1
POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_DN | 51 | 48 | 0.941176470588235 | 2 | 12.5084665358539 | 0.0128151494966953 | 1 | SLC1A2 OLFM1
HUANG_DASATINIB_RESISTANCE_DN | 58 | 48 | 0.827586206896552 | 2 | 12.5084665358539 | 0.0128151494966953 | 1 | C14orf93 SLC1A2
PEPTIDE_RECEPTOR_ACTIVITY | 50 | 49 | 0.98 | 2 | 12.2428874053849 | 0.0133300869651016 | 1 | NPBWR2 SSTR5
module_234 | 53 | 52 | 0.981132075471698 | 2 | 11.5064749896014 | 0.0149280785650253 | 1 | DLX5 MSX1
HUPER_BREAST_BASAL_VS_LUMINAL_UP | 54 | 54 | 1 | 2 | 11.0627212798932 | 0.0160370470997662 | 1 | [NAME]
LEE_LIVER_CANCER_CIPROFIBRATE_UP | 58 | 55 | 0.948275862068966 | 2 | 10.8547734394412 | 0.0166044229076123 | 1 | [NAME]
TESAR_ALK_TARGETS_HUMAN_ES_5D_UP | 5 | 5 | 1 | 1 | 70.5125235425599 | 0.0178114231891895 | 1 | MSX1
HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_DN | 63 | 59 | 0.936507936507937 | 2 | 10.0879070483601 | 0.0189583291861714 | 1 | MS4A3 PRTN3
ZHU_CMV_ALL_UP | 60 | 59 | 0.983333333333333 | 2 | 10.0879070483601 | 0.0189583291861714 | 1 | GAL MSX1
NIKOLSKY_BREAST_CANCER_7Q21_Q22_AMPLICON | 76 | 60 | 0.789473684210526 | 2 | 9.91418071207964 | 0.0195675798684451 | 1 | PPP1R9A DLX5
chr9q34 | 228 | 162 | 0.710526315789474 | 3 | 5.49923868040834 | 0.0203068295968392 | 1 | FCN2 FCN1 OLFM1
V$E2A_Q2 | 182 | 162 | 0.89010989010989 | 3 | 5.49923868040834 | 0.0203068295968392 | 1 | SELPLG SH3TC1 CBFA2T3
TCTATGA,MIR-376A,MIR-376B | 72 | 62 | 0.861111111111111 | 2 | 9.58316849401466 | 0.0208105576735932 | 1 | DLX5 [NAME]
REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS | 173 | 165 | 0.953757225433526 | 3 | 5.39632774643314 | 0.0213036951810904 | 1 | GAL NPBWR2 SSTR5
NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_UP | 6 | 6 | 1 | 1 | 56.4638449345094 | 0.0213361855076267 | 1 | DLX5
REACTOME_G_ALPHA_I_SIGNALLING_EVENTS | 177 | 167 | 0.943502824858757 | 3 | 5.32979113447314 | 0.0219830355807684 | 1 | GAL NPBWR2 SSTR5
LOPEZ_MBD_TARGETS | 873 | 795 | 0.910652920962199 | 7 | 2.69545986283013 | 0.0226316797391915 | 1 | GAL SELPLG FCN1 SLC22A18 PARVG VHL SERPINA1
MORF_MYC | 72 | 65 | 0.902777777777778 | 2 | 9.12627394886167 | 0.0227352586193147 | 1 | MSX1 SSTR5
FERNANDEZ_BOUND_BY_MYC | 176 | 171 | 0.971590909090909 | 3 | 5.20102332569057 | 0.023377170706766 | 1 | GAL VHL PRTN3
TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN | 186 | 172 | 0.924731182795699 | 3 | 5.17016923214158 | 0.0237330925869965 | 1 | MS4A3 SELPLG CBFA2T3
BASAKI_YBX1_TARGETS_DN | 370 | 306 | 0.827027027027027 | 4 | 3.90138414073153 | 0.023847259454607 | 1 | PPP1R9A [NAME]
CARBOHYDRATE_BINDING | 72 | 67 | 0.930555555555556 | 2 | 8.84365006775881 | 0.0240578123730958 | 1 | FCN2 FCN1
V$ETS1_B | 188 | 174 | 0.925531914893617 | 3 | 5.10780687849844 | 0.0244538022654383 | 1 | [NAME]
SAMOLS_TARGETS_OF_KHSV_MIRNAS_UP | 8 | 7 | 0.875 | 1 | 47.0429549548585 | 0.0248485409740913 | 1 | GAL
YE_METASTATIC_LIVER_CANCER | 7 | 7 | 1 | 1 | 47.0429549548585 | 0.0248485409740913 | 1 | SERPINB5
V$ICSBP_Q6 | 190 | 176 | 0.926315789473684 | 3 | 5.04834018709044 | 0.0251863315493144 | 1 | BST2 CITED4 MSX1
WU_CELL_MIGRATION | 183 | 177 | 0.967213114754098 | 3 | 5.01908189501381 | 0.0255570274923985 | 1 | BST2 MEST SERPINB5
[NAME] | 85 | 70 | 0.823529411764706 | 2 | 8.45294191549073 | 0.026099527014995 | 1 | ST6GALNAC1 MSX1
WALLACE_PROSTATE_CANCER_RACE_DN | 87 | 71 | 0.816091954022989 | 2 | 8.32852328846251 | 0.0267952881351441 | 1 | [NAME]
[NAME] | 75 | 71 | 0.946666666666667 | 2 | 8.32852328846251 | 0.0267952881351441 | 1 | HNF4A [NAME]
MORF_FDXR | 207 | 182 | 0.879227053140097 | 3 | 4.87747357975469 | 0.0274547918033397 | 1 | SSTR5 TUBGCP2 MSX1
CELL_PROLIFERATION_GO_0008283 | 501 | 478 | 0.954091816367265 | 5 | 3.14154281366258 | 0.0278462452983546 | 1 | SSTR5 CBFA2T3 BST2 VHL PRTN3
DORN_ADENOVIRUS_INFECTION_24HR_UP | 8 | 8 | 1 | 1 | 40.3448467228486 | 0.0283485324062662 | 1 | SERPINB5
REACTOME_RECRUITMENT_OF_NUMA_TO_MITOTIC_CENTROSOMES | 11 | 8 | 0.727272727272727 | 1 | 40.3448467228486 | 0.0283485324062662 | 1 | TUBGCP2
RICKMAN_HEAD_AND_NECK_CANCER_E | 87 | 75 | 0.862068965517241 | 2 | 7.87047143568475 | 0.0296526611412753 | 1 | ST6GALNAC1 [NAME]
[NAME] | 86 | 76 | 0.883720930232558 | 2 | 7.76366328371872 | 0.0303852865321685 | 1 | MSX1 SSTR5
RESPONSE_TO_TOXIN | 10 | 9 | 0.9 | 1 | 35.2997998033212 | 0.0318362024770102 | 1 | [NAME]
module_165 | 78 | 78 | 1 | 2 | 7.5585528820669 | 0.0318720603696061 | 1 | FCN1 PRTN3
ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP | 218 | 195 | 0.894495412844037 | 3 | 4.54347317371171 | 0.0327334398981165 | 1 | TRIM15 [NAME]
V$OCT_C | 212 | 196 | 0.924528301886792 | 3 | 4.51957142603461 | 0.0331600175002331 | 1 | [NAME]
PEPTIDE_BINDING | 82 | 80 | 0.975609756097561 | 2 | 7.36408357275528 | 0.0333871406428381 | 1 | NPBWR2 SSTR5
module_84 | 531 | 504 | 0.949152542372881 | 5 | 2.9723507884535 | 0.0339001626795348 | 1 | FCN1 MS4A7 CES1 SELPLG SERPINA1
ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION | 87 | 82 | 0.942528735632184 | 2 | 7.1794703383922 | 0.0349300625781749 | 1 | OLFM1 MSX1
RGAGGAARY_V$PU1_Q6 | 380 | 346 | 0.910526315789474 | 4 | 3.43535642659593 | 0.0352185163822215 | 1 | [NAME] SH3TC1
MCCOLLUM_GELDANAMYCIN_RESISTANCE_UP | 10 | 10 | 1 | 1 | 31.3897108011105 | 0.0353115937148402 | 1 | ST6GALNAC1
WU_ALZHEIMER_DISEASE_UP | 11 | 10 | 0.909090909090909 | 1 | 31.3897108011105 | 0.0353115937148402 | 1 | CBFA2T3
GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_2 | 11 | 10 | 0.909090909090909 | 1 | 31.3897108011105 | 0.0353115937148402 | 1 | MS4A3
JAATINEN_HEMATOPOIETIC_STEM_CELL_DN | 222 | 206 | 0.927927927927928 | 3 | 4.29378270354682 | 0.0375859574579782 | 1 | FCN1 [NAME]
GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_DN | 11 | 11 | 1 | 1 | 28.2609012978036 | 0.0387747485044037 | 1 | MS4A3
HOEGERKORP_CD44_TARGETS_DIRECT_DN | 11 | 11 | 1 | 1 | 28.2609012978036 | 0.0387747485044037 | 1 | SERPINA1
ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_UP | 141 | 87 | 0.617021276595745 | 2 | 6.75363378818357 | 0.0389061694149148 | 1 | MS4A3 SPRR1A
RIGGI_EWING_SARCOMA_PROGENITOR_UP | 413 | 358 | 0.86682808716707 | 4 | 3.31609174221469 | 0.0391525955743054 | 1 | BST2 CES1 MSX1 SH3TC1
ORGAN_DEVELOPMENT | 567 | 528 | 0.931216931216931 | 5 | 2.83110424548863 | 0.0401709924206472 | 1 | DLX5 MEST TRIM15 MSX1 SPRR1A
CALCIUM_ION_BINDING | 100 | 90 | 0.9 | 2 | 6.52256818899285 | 0.0413710447793622 | 1 | FCN2 FCN1
HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP | 403 | 365 | 0.905707196029777 | 4 | 3.25018057751423 | 0.0415601058169698 | 1 | [NAME]
[NAME] | 17 | 12 | 0.705882352941177 | 1 | 25.6961965912109 | 0.0422257090869619 | 1 | [NAME]
SA_PROGRAMMED_CELL_DEATH | 12 | 12 | 1 | 1 | 25.6961965912109 | 0.0422257090869619 | 1 | [NAME]
DELAYED_RECTIFIER_POTASSIUM_CHANNEL_ACTIVITY | 12 | 12 | 1 | 1 | 25.6961965912109 | 0.0422257090869619 | 1 | KCNQ1
[NAME] | 100 | 93 | 0.93 | 2 | 6.30627297577219 | 0.0438935023075145 | 1 | BST2 MSX1
IMMUNE_RESPONSE | 232 | 220 | 0.948275862068966 | 3 | 4.01294618284387 | 0.0442666883404109 | 1 | FCN2 FCN1 BST2
NIKOLSKY_BREAST_CANCER_16P13_AMPLICON | 120 | 95 | 0.791666666666667 | 2 | 6.16982495608869 | 0.0456064057759443 | 1 | [NAME]
YAMASHITA_LIVER_CANCER_WITH_EPCAM_DN | 14 | 13 | 0.928571428571429 | 1 | 23.5578661082396 | 0.0456645175608602 | 1 | [NAME]
CORNIFIED_ENVELOPE | 13 | 13 | 1 | 1 | 23.5578661082396 | 0.0456645175608602 | 1 | SPRR1A
CELL_FATE_COMMITMENT | 13 | 13 | 1 | 1 | 23.5578661082396 | 0.0456645175608602 | 1 | TRIM15
SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 | 415 | 377 | 0.908433734939759 | 4 | 3.14294405823804 | 0.0458807253626287 | 1 | BST2 HNF4A MSX1 SERPINA1
module_177 | 101 | 97 | 0.96039603960396 | 2 | 6.0391572010116 | 0.0473438207157308 | 1 | BST2 VHL
module_75 | 391 | 384 | 0.982097186700767 | 4 | 3.08353257196785 | 0.0485139416469368 | 1 | FCN2 FCN1 BST2 CES1
LEE_INTRATHYMIC_T_PROGENITOR | 15 | 14 | 0.933333333333333 | 1 | 21.7253695173442 | 0.0490912158820062 | 1 | MEST
BIOCARTA_GRANULOCYTES_PATHWAY | 14 | 14 | 1 | 1 | 21.7253695173442 | 0.0490912158820062 | 1 | SELPLG
TISSUE_MORPHOGENESIS | 14 | 14 | 1 | 1 | 21.7253695173442 | 0.0490912158820062 | 1 | TRIM15
[NAME] | 15 | 14 | 0.933333333333333 | 1 | 21.7253695173442 | 0.0490912158820062 | 1 | SPRR1A
VERHAAK_AML_WITH_NPM1_MUTATED_DN | 246 | 234 | 0.951219512195122 | 3 | 3.76624012302583 | 0.0515020165405014 | 1 | MS4A3 MEST PRTN3
LIU_BREAST_CANCER | 16 | 15 | 0.9375 | 1 | 20.1823793467251 | 0.0525058458643375 | 1 | FCN2
BIOCARTA_HIF_PATHWAY | 15 | 15 | 1 | 1 | 20.1823793467251 | 0.0525058458643375 | 1 | VHL
[NAME] | 16 | 15 | 0.9375 | 1 | 20.1823793467251 | 0.0525058458643375 | 1 | [NAME]