category_id category_display_name macrogroup_id macrogroup_name macrogroup_order category_order_within_macrogroup color n_genesets n_genesets_mapped n_genesets_evaluable n_genesets_significant n_pos_genesets n_neg_genesets mean_NES mean_NES_contextual mean_pos_NES mean_neg_NES median_NES consistency min_padj min_padj_mapped has_significant_support gsea_padj_cutoff same_direction_pct mean_NES_direction analysis figure_type source_row_order selected_for_plot group_by_supracategory plot_order annotation_variant figure_title_encoded figure_subtitle_encoded positive_direction_encoded figure_width figure_height figure_dpi figure_background analysis_id collection n_sets_total n_sets_eligible n_sets_evaluable n_sets_missing_p n_sets_not_eligible_or_absent coverage_pct category_p_adjusted minimum_enriched_sets minimum_enriched_pct significant status n_positive_NES n_negative_NES n_zero_NES n_missing_NES alpha confidence_level family_size family_scope method family_id support_schema_version support_grade support_label minimum_support_pct_text support_count support_annotation observed_NES_pattern observed_NES_counts has_lollipop_geometry hommel_support_schema DEVELOPMENT_MORPHOGENESIS Development and morphogenesis DEVELOPMENT_NEURAL Developmental and neural programs 4 1 #E88BA1 96 1010 365 96 73 23 0.83096522712310295 0.42973606935143499 1.5554053225036399 -1.4683446408238301 1.4379224067931899 0.76041666666666696 2.0768143478540701e-12 2.0768143478540701e-12 TRUE 0.25 76 Positive NES GSEA lisa_lollipop 1 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 1010 365 365 0 645 36.138613861386141 9.7896252699664202e-09 7 1.9178082191780821 TRUE significant 247 118 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 1.91% 7/365 S1 · ≥1.91% · 7/365 Observed NES of both signs +247 / -118 / zero 0 / missing 0; N=365 TRUE hommel-support-ui-v1 NEUROGENESIS_SYNAPSE Neurogenesis and synapse DEVELOPMENT_NEURAL Developmental and neural programs 4 2 #B9576E 57 791 272 57 33 24 0.26921833170288301 0.053820156733371302 1.59313664620538 -1.55116935073805 1.2882522416226501 0.57894736842105299 8.6199681133542604e-09 8.6199681133542604e-09 TRUE 0.25 57.899999999999999 Positive NES GSEA lisa_lollipop 2 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 791 272 272 0 519 34.386852085967128 1.7183020254170389e-05 4 1.4705882352941178 TRUE significant 138 134 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 1.47% 4/272 S1 · ≥1.47% · 4/272 Observed NES of both signs +138 / -134 / zero 0 / missing 0; N=272 TRUE hommel-support-ui-v1 DNA_DAMAGE_REPAIR_CHECKPOINTS DNA damage, repair and checkpoints GENOME_GENE_EXPRESSION Genome and gene expression 7 1 #D99A66 140 295 162 140 140 0 1.8072464246609501 1.67141747845804 1.8072464246609501 1.86222449479942 1 4.4021540872392203e-15 4.4021540872392203e-15 TRUE 0.25 100 Positive NES GSEA lisa_lollipop 3 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 295 162 162 0 133 54.915254237288138 6.2991409127062473e-12 9 5.5555555555555554 TRUE significant 159 3 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 5.55% 9/162 S1 · ≥5.55% · 9/162 Observed NES of both signs +159 / -3 / zero 0 / missing 0; N=162 TRUE hommel-support-ui-v1 RNA_PROCESSING_SPLICING_RNP RNA processing and RNP biology GENOME_GENE_EXPRESSION Genome and gene expression 7 2 #D18649 96 263 152 96 86 10 1.3629898647186101 1.0547476426435201 1.75125204083543 -1.97606484988606 1.6252572794228199 0.89583333333333304 2.1826667627702798e-21 2.1826667627702798e-21 TRUE 0.25 89.599999999999994 Positive NES GSEA lisa_lollipop 4 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 263 152 152 0 111 57.79467680608365 7.6221036829694192e-19 12 7.8947368421052628 TRUE significant 129 23 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 7.89% 12/152 S1 · ≥7.89% · 12/152 Observed NES of both signs +129 / -23 / zero 0 / missing 0; N=152 TRUE hommel-support-ui-v1 TRANSCRIPTION_CHROMATIN_EPIGENETICS Transcription, chromatin and epigenetics GENOME_GENE_EXPRESSION Genome and gene expression 7 3 #C17537 104 416 213 104 103 1 1.5998865493916401 1.1524065618729999 1.62980665336407 -1.4818841597693699 1.61263006080275 0.99038461538461497 6.1409688463193302e-12 6.1409688463193302e-12 TRUE 0.25 99 Positive NES GSEA lisa_lollipop 5 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 416 213 213 0 203 51.20192307692308 7.1532779652132888e-09 6 2.816901408450704 TRUE significant 193 20 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 2.81% 6/213 S1 · ≥2.81% · 6/213 Observed NES of both signs +193 / -20 / zero 0 / missing 0; N=213 TRUE hommel-support-ui-v1 TRANSLATION_RIBOSOME Translation and ribosome GENOME_GENE_EXPRESSION Genome and gene expression 7 4 #A96730 46 116 73 46 32 14 0.82597651492911806 0.64999733160217399 2.17090525931579 -2.24814632938328 1.8414589572754301 0.69565217391304301 2.6847743929669401e-40 2.6847743929669401e-40 TRUE 0.25 69.599999999999994 Positive NES GSEA lisa_lollipop 6 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 116 73 73 0 43 62.931034482758619 9.1367447322431598e-39 22 30.136986301369863 TRUE significant 50 23 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S3 Supported in at least one quarter 30.13% 22/73 S3 · ≥30.13% · 22/73 Observed NES of both signs +50 / -23 / zero 0 / missing 0; N=73 TRUE hommel-support-ui-v1 IMMUNE_ADAPTIVE_ANTIGEN_MHC Adaptive immunity and antigen presentation IMMUNE_INFLAMMATION Immune and inflammatory biology 8 1 #BDA838 142 328 153 142 141 1 2.0504615342333401 1.9722711624095699 2.07404955544696 -1.27544945688592 2.0992480779283 0.99295774647887303 7.5531201600068901e-19 7.5531201600068901e-19 TRUE 0.25 99.299999999999997 Positive NES GSEA lisa_lollipop 7 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 328 153 153 0 175 46.646341463414636 8.9225728388411436e-16 38 24.836601307189543 TRUE significant 151 2 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S2 Supported in at least one tenth 24.83% 38/153 S2 · ≥24.83% · 38/153 Observed NES of both signs +151 / -2 / zero 0 / missing 0; N=153 TRUE hommel-support-ui-v1 IMMUNE_CYTOKINE_INFLAMMATORY Cytokine and inflammatory signaling IMMUNE_INFLAMMATION Immune and inflammatory biology 8 2 #B09812 200 535 250 200 198 2 1.8971294529465501 1.69294725213249 1.93083700255623 -1.43991795841243 1.89927822163958 0.98999999999999999 8.3973899298373499e-23 8.3973899298373499e-23 TRUE 0.25 99 Positive NES GSEA lisa_lollipop 8 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 535 250 250 0 285 46.728971962616825 1.8957001829404835e-20 35 14 TRUE significant 241 9 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S2 Supported in at least one tenth 14% 35/250 S2 · ≥14% · 35/250 Observed NES of both signs +241 / -9 / zero 0 / missing 0; N=250 TRUE hommel-support-ui-v1 IMMUNE_CORE Immune core IMMUNE_INFLAMMATION Immune and inflammatory biology 8 3 #9F8700 104 185 110 104 104 0 2.0501522851351801 1.9605116407694601 2.0501522851351801 2.09363931101892 1 1.0124495021119301e-21 1.0124495021119301e-21 TRUE 0.25 100 Positive NES GSEA lisa_lollipop 9 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 185 110 110 0 75 59.45945945945946 4.3435172172594002e-19 43 39.090909090909093 TRUE significant 108 2 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S3 Supported in at least one quarter 39.09% 43/110 S3 · ≥39.09% · 43/110 Observed NES of both signs +108 / -2 / zero 0 / missing 0; N=110 TRUE hommel-support-ui-v1 IMMUNE_INNATE_COMPLEMENT_PRR Innate immunity, complement and PRR IMMUNE_INFLAMMATION Immune and inflammatory biology 8 4 #8B7600 103 308 151 103 103 0 1.8252204388154201 1.41938581084356 1.8252204388154201 1.8509671449988001 1 3.93590197944892e-12 3.93590197944892e-12 TRUE 0.25 100 Positive NES GSEA lisa_lollipop 10 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 308 151 151 0 157 49.025974025974023 4.3970352109615825e-09 9 5.9602649006622519 TRUE significant 137 14 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 5.96% 9/151 S1 · ≥5.96% · 9/151 Observed NES of both signs +137 / -14 / zero 0 / missing 0; N=151 TRUE hommel-support-ui-v1 METABOLISM_AA_ONECARBON Amino acid and one-carbon metabolism METABOLISM_BIOENERGETICS Metabolism and bioenergetics 12 1 #8FB438 81 251 99 81 5 76 -1.7037433994575499 -1.4949417911554801 1.5433009977719401 -1.9173647413805399 -1.7733827636275501 0.938271604938272 6.08674105869893e-19 6.08674105869893e-19 TRUE 0.25 93.799999999999997 Negative NES GSEA lisa_lollipop 11 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 251 99 99 0 152 39.442231075697208 3.0078475350389054e-16 15 15.151515151515152 TRUE significant 10 89 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S2 Supported in at least one tenth 15.15% 15/99 S2 · ≥15.15% · 15/99 Observed NES of both signs +10 / -89 / zero 0 / missing 0; N=99 TRUE hommel-support-ui-v1 METABOLISM_CARBOHYDRATE_GLYCOLYSIS Carbohydrate metabolism and glycolysis METABOLISM_BIOENERGETICS Metabolism and bioenergetics 12 2 #85AE28 40 172 86 40 22 18 0.21656069294253899 0.169829031758685 1.70644455982853 -1.6044084776959 1.27040138140875 0.55000000000000004 9.0731865541434704e-06 9.0731865541434704e-06 TRUE 0.25 55 Positive NES GSEA lisa_lollipop 12 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 172 86 86 0 86 50 0.037004200289129603 1 1.1627906976744187 TRUE significant 48 38 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 1.16% 1/86 S1 · ≥1.16% · 1/86 Observed NES of both signs +48 / -38 / zero 0 / missing 0; N=86 TRUE hommel-support-ui-v1 DETOX_XENOBIOTIC_METABOLISM Detoxification and xenobiotic metabolism METABOLISM_BIOENERGETICS Metabolism and bioenergetics 12 3 #7CA818 34 126 55 34 2 32 -1.5122763315730601 -1.0700731043077201 1.8688619836310201 -1.7235974762733199 -1.7101778800687499 0.94117647058823495 7.8326208934477201e-06 7.8326208934477201e-06 TRUE 0.25 94.099999999999994 Negative NES GSEA lisa_lollipop 13 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 126 55 55 0 71 43.650793650793652 0.027222291070191789 1 1.8181818181818181 TRUE significant 9 46 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 1.81% 1/55 S1 · ≥1.81% · 1/55 Observed NES of both signs +9 / -46 / zero 0 / missing 0; N=55 TRUE hommel-support-ui-v1 METABOLISM_CORE General metabolism METABOLISM_BIOENERGETICS Metabolism and bioenergetics 12 4 #73A208 13 51 34 13 3 10 -1.2288523092132599 -0.58317792429545301 1.36424204754656 -2.0067806162412101 -1.7958694010033101 0.76923076923076905 7.3243271077311301e-23 7.3243271077311301e-23 TRUE 0.25 76.900000000000006 Negative NES GSEA lisa_lollipop 14 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 51 34 34 0 17 66.666666666666671 4.0854721762775964e-20 6 17.647058823529413 TRUE significant 12 22 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S2 Supported in at least one tenth 17.64% 6/34 S2 · ≥17.64% · 6/34 Observed NES of both signs +12 / -22 / zero 0 / missing 0; N=34 TRUE hommel-support-ui-v1 METABOLISM_LIPID_FA Lipid and fatty acid metabolism METABOLISM_BIOENERGETICS Metabolism and bioenergetics 12 5 #6C9A00 119 637 291 119 19 100 -1.2584554400533201 -0.59987918856515798 1.5459395025298801 -1.79129047914413 -1.61868334308708 0.84033613445378197 7.3237062734336499e-25 7.3237062734336499e-25 TRUE 0.25 84 Negative NES GSEA lisa_lollipop 15 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 637 291 291 0 346 45.682888540031399 1.1596376749753847e-22 17 5.8419243986254292 TRUE significant 94 197 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 5.84% 17/291 S1 · ≥5.84% · 17/291 Observed NES of both signs +94 / -197 / zero 0 / missing 0; N=291 TRUE hommel-support-ui-v1 MITOCHONDRIA_OXPHOS_ETC Mitochondria, OXPHOS and ETC METABOLISM_BIOENERGETICS Metabolism and bioenergetics 12 6 #669200 80 143 95 80 0 80 -2.44438911166143 -2.11079271209563 -2.44438911166143 -2.3617621525655101 1 2.1045494711586399e-48 2.1045494711586399e-48 TRUE 0.25 100 Negative NES GSEA lisa_lollipop 16 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 143 95 95 0 48 66.43356643356644 2.388172549384355e-47 44 46.315789473684212 TRUE significant 5 90 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S3 Supported in at least one quarter 46.31% 44/95 S3 · ≥46.31% · 44/95 Observed NES of both signs +5 / -90 / zero 0 / missing 0; N=95 TRUE hommel-support-ui-v1 METABOLISM_NUCLEOTIDE Nucleotide metabolism METABOLISM_BIOENERGETICS Metabolism and bioenergetics 12 7 #608A00 32 175 91 32 22 10 0.31427740975485602 0.41202890933217901 1.54179957648508 -2.3862713570516401 1.4185318981019801 0.6875 4.8833941120846899e-20 4.8833941120846899e-20 TRUE 0.25 68.799999999999997 Positive NES GSEA lisa_lollipop 17 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 175 91 91 0 84 52 1.9770793736346569e-17 11 12.087912087912088 TRUE significant 63 28 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S2 Supported in at least one tenth 12.08% 11/91 S2 · ≥12.08% · 11/91 Observed NES of both signs +63 / -28 / zero 0 / missing 0; N=91 TRUE hommel-support-ui-v1 PEROXISOME_FAO Peroxisome and fatty acid oxidation METABOLISM_BIOENERGETICS Metabolism and bioenergetics 12 8 #5B8200 8 21 9 8 0 8 -1.9486515175280399 -1.8782331501098699 -1.9486515175280399 -1.9315486976498799 1 1.7689159935435501e-08 1.7689159935435501e-08 TRUE 0.25 100 Negative NES GSEA lisa_lollipop 18 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 21 9 9 0 12 42.857142857142854 9.0190009274021264e-05 2 22.222222222222221 TRUE significant 0 9 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S2 Supported in at least one tenth 22.22% 2/9 S2 · ≥22.22% · 2/9 Observed negative NES +0 / -9 / zero 0 / missing 0; N=9 TRUE hommel-support-ui-v1 ECM_MATRIX_REMODELING ECM and matrix remodeling MICROENVIRONMENT_VASCULAR_ECM Microenvironment, vascular and ECM 13 1 #38BD7E 25 183 79 25 17 8 0.63654426533528896 0.41625525756418902 1.6574052614620001 -1.53278535143397 1.4550990693175001 0.68000000000000005 0.00037014269835389301 0.00037014269835389301 TRUE 0.25 68 Positive NES GSEA lisa_lollipop 19 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 183 79 79 0 104 43.169398907103826 1 0 0 FALSE not_significant 54 25 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 No minimum greater than zero could be supported 0% 0/79 Observed NES of both signs +54 / -25 / zero 0 / missing 0; N=79 TRUE hommel-support-ui-v1 VASCULAR_LYMPHATIC Vascular, angiogenic and lymphatic biology MICROENVIRONMENT_VASCULAR_ECM Microenvironment, vascular and ECM 13 2 #008B4A 26 151 72 26 23 3 1.2786002345796299 0.72490033507801899 1.63499240154797 -1.4537397121775799 1.5404334948889999 0.88461538461538503 2.95554789725402e-06 2.95554789725402e-06 TRUE 0.25 88.5 Positive NES GSEA lisa_lollipop 20 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 151 72 72 0 79 47.682119205298015 0.01102531841175077 2 2.7777777777777777 TRUE significant 55 17 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 2.77% 2/72 S1 · ≥2.77% · 2/72 Observed NES of both signs +55 / -17 / zero 0 / missing 0; N=72 TRUE hommel-support-ui-v1 CELL_CYCLE_PROLIFERATION Cell cycle and proliferation PROLIFERATION_CELL_CYCLE Proliferation and cell cycle 16 1 #00AD9A 169 555 257 169 169 0 1.7369274995871 1.3357441716371099 1.7369274995871 1.6878252042911499 1 7.9991233579409494e-14 7.9991233579409494e-14 TRUE 0.25 100 Positive NES GSEA lisa_lollipop 21 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 555 257 257 0 298 46.306306306306304 7.3173913685514825e-11 21 8.1712062256809332 TRUE significant 235 22 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 8.17% 21/257 S1 · ≥8.17% · 21/257 Observed NES of both signs +235 / -22 / zero 0 / missing 0; N=257 TRUE hommel-support-ui-v1 SIGNALING_CORE Core cell signaling SIGNALING_COMMUNICATION Signaling and cell communication 20 1 #38BAD6 160 714 378 160 158 2 1.5876304859036601 0.91936203874287103 1.6281927371895599 -1.6167873656827401 1.5649431927325099 0.98750000000000004 2.0458743260219301e-23 2.0458743260219301e-23 TRUE 0.25 98.799999999999997 Positive NES GSEA lisa_lollipop 22 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 714 378 378 0 336 52.941176470588232 3.9296821242093988e-21 4 1.0582010582010581 TRUE significant 310 68 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 1.05% 4/378 S1 · ≥1.05% · 4/378 Observed NES of both signs +310 / -68 / zero 0 / missing 0; N=378 TRUE hommel-support-ui-v1 ENDOCRINE_HORMONAL Endocrine and hormonal pathways SIGNALING_COMMUNICATION Signaling and cell communication 20 2 #1CB0D0 64 497 192 64 41 23 0.44505880750850602 0.062140600534978899 1.5834051607557 -1.5841673004538801 1.3846528921911101 0.640625 1.5539821892518201e-06 1.5539821892518201e-06 TRUE 0.25 64.099999999999994 Positive NES GSEA lisa_lollipop 23 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 497 192 192 0 305 38.631790744466798 0.0046200025723519295 1 0.52083333333333337 TRUE significant 98 94 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 0.52% 1/192 S1 · ≥0.52% · 1/192 Observed NES of both signs +98 / -94 / zero 0 / missing 0; N=192 TRUE hommel-support-ui-v1 GROWTH_FACTOR_RTK Growth factor and RTK pathways SIGNALING_COMMUNICATION Signaling and cell communication 20 3 #00A6CA 129 412 225 129 128 1 1.5928438358855299 1.23843159357955 1.61796536147305 -1.62271143931629 1.59702947875761 0.99224806201550397 0.00062457722441825304 0.00062457722441825304 TRUE 0.25 99.200000000000003 Positive NES GSEA lisa_lollipop 24 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 412 225 225 0 187 54.61165048543689 1 0 0 FALSE not_significant 209 16 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 No minimum greater than zero could be supported 0% 0/225 Observed NES of both signs +209 / -16 / zero 0 / missing 0; N=225 TRUE hommel-support-ui-v1 TGFB_SMAD TGF-beta and SMAD signaling SIGNALING_COMMUNICATION Signaling and cell communication 20 4 #0097B8 8 129 57 8 8 0 1.5383466431413699 0.60162261912067705 1.5383466431413699 1.4785049829878401 1 0.00475532866351875 0.00475532866351875 TRUE 0.25 100 Positive NES GSEA lisa_lollipop 25 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 129 57 57 0 72 44.186046511627907 1 0 0 FALSE not_significant 43 14 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 No minimum greater than zero could be supported 0% 0/57 Observed NES of both signs +43 / -14 / zero 0 / missing 0; N=57 TRUE hommel-support-ui-v1 WNT_NOTCH_HEDGEHOG_HIPPO Wnt, Notch, Hedgehog and Hippo SIGNALING_COMMUNICATION Signaling and cell communication 20 5 #0088A6 26 263 97 26 26 0 1.5771106219843201 0.85228949220823702 1.5771106219843201 1.5768943778536699 1 0.00033089439394481902 0.00033089439394481902 TRUE 0.25 100 Positive NES GSEA lisa_lollipop 26 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 263 97 97 0 166 36.882129277566541 1 0 0 FALSE not_significant 82 15 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 No minimum greater than zero could be supported 0% 0/97 Observed NES of both signs +82 / -15 / zero 0 / missing 0; N=97 TRUE hommel-support-ui-v1 APOPTOSIS_CELL_DEATH Apoptosis and regulated cell death STRESS_DEATH_PROTEOSTASIS Stress, proteostasis and cell death 22 1 #7EA9EA 106 321 162 106 104 2 1.68142757865851 1.19399641897756 1.75895993174473 -2.3502547818250599 1.69703453790893 0.98113207547169801 4.6642967691587999e-22 4.6642967691587999e-22 TRUE 0.25 98.099999999999994 Positive NES GSEA lisa_lollipop 27 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 321 162 162 0 159 50.467289719626166 3.6592930047509023e-19 9 5.5555555555555554 TRUE significant 138 24 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 5.55% 9/162 S1 · ≥5.55% · 9/162 Observed NES of both signs +138 / -24 / zero 0 / missing 0; N=162 TRUE hommel-support-ui-v1 AUTOPHAGY_LYSOSOME Autophagy, lysosome and phagosome maturation STRESS_DEATH_PROTEOSTASIS Stress, proteostasis and cell death 22 2 #71A1E8 24 154 92 24 15 9 0.38332743895692201 0.14296295550277499 1.6470282832512799 -1.72284063486701 1.4518309056826799 0.625 2.62162073970218e-08 2.62162073970218e-08 TRUE 0.25 62.5 Positive NES GSEA lisa_lollipop 28 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 154 92 92 0 62 59.740259740259738 0.00013140496152188309 1 1.0869565217391304 TRUE significant 50 42 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 1.08% 1/92 S1 · ≥1.08% · 1/92 Observed NES of both signs +50 / -42 / zero 0 / missing 0; N=92 TRUE hommel-support-ui-v1 ER_STRESS_UPR ER stress and unfolded protein response STRESS_DEATH_PROTEOSTASIS Stress, proteostasis and cell death 22 3 #6599E6 8 48 25 8 8 0 1.62421587115815 1.16952780115572 1.62421587115815 1.6686003092774699 1 0.00062959965893430296 0.00062959965893430296 TRUE 0.25 100 Positive NES GSEA lisa_lollipop 29 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 48 25 25 0 23 52.083333333333336 1 0 0 FALSE not_significant 25 0 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 No minimum greater than zero could be supported 0% 0/25 Observed positive NES +25 / -0 / zero 0 / missing 0; N=25 TRUE hommel-support-ui-v1 HEAT_SHOCK_STRESS_RESPONSE Heat shock and acute stress response STRESS_DEATH_PROTEOSTASIS Stress, proteostasis and cell death 22 4 #5991E4 4 17 12 4 4 0 1.5770252727138001 0.88537707935051602 1.5770252727138001 1.5790315311249601 1 0.00116564723123458 0.00116564723123458 TRUE 0.25 100 Positive NES GSEA lisa_lollipop 30 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 17 12 12 0 5 70.588235294117652 1 0 0 FALSE not_significant 11 1 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 No minimum greater than zero could be supported 0% 0/12 Observed NES of both signs +11 / -1 / zero 0 / missing 0; N=12 TRUE hommel-support-ui-v1 HYPOXIA_HIF Hypoxia and HIF programs STRESS_DEATH_PROTEOSTASIS Stress, proteostasis and cell death 22 5 #5388D6 10 31 14 10 10 0 1.6376544632855801 1.5021386704255899 1.6376544632855801 1.71096601692092 1 0.00107558033211133 0.00107558033211133 TRUE 0.25 100 Positive NES GSEA lisa_lollipop 31 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 31 14 14 0 17 45.161290322580648 1 0 0 FALSE not_significant 14 0 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 No minimum greater than zero could be supported 0% 0/14 Observed positive NES +14 / -0 / zero 0 / missing 0; N=14 TRUE hommel-support-ui-v1 OXIDATIVE_STRESS_REDOX_ROS Oxidative stress, redox and ROS STRESS_DEATH_PROTEOSTASIS Stress, proteostasis and cell death 22 6 #4E7FC8 25 116 74 25 17 8 0.64881875383960497 0.22591083005005 1.66657712361383 -1.51391778193062 1.3607480512250001 0.68000000000000005 6.5115749771887198e-05 6.5115749771887198e-05 TRUE 0.25 68 Positive NES GSEA lisa_lollipop 32 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 116 74 74 0 42 63.793103448275865 0.44689810124235008 0 0 FALSE not_significant 40 34 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 No minimum greater than zero could be supported 0% 0/74 Observed NES of both signs +40 / -34 / zero 0 / missing 0; N=74 TRUE hommel-support-ui-v1 PROTEOSTASIS_UBIQUITIN_PROTEASOME Proteostasis, ubiquitin and proteasome STRESS_DEATH_PROTEOSTASIS Stress, proteostasis and cell death 22 7 #4977BB 91 214 142 91 89 2 1.49374219985581 1.16332032576391 1.58133972643193 -2.4043477327815901 1.5671844051717601 0.97802197802197799 8.7091270678172797e-24 8.7091270678172797e-24 TRUE 0.25 97.799999999999997 Positive NES GSEA lisa_lollipop 33 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 214 142 142 0 72 66.355140186915889 3.0993721719145963e-21 3 2.112676056338028 TRUE significant 129 13 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 2.11% 3/142 S1 · ≥2.11% · 3/142 Observed NES of both signs +129 / -13 / zero 0 / missing 0; N=142 TRUE hommel-support-ui-v1 ADHESION_JUNCTION_POLARITY Adhesion, junctions and polarity STRUCTURE_MOTILITY_PLASTICITY Structure, motility and plasticity 24 1 #C693E7 71 260 150 71 64 7 1.4206341253863199 0.64148382232692502 1.7364073819013801 -1.4664356484656 1.5601983898170899 0.90140845070422504 2.65496260478752e-16 2.65496260478752e-16 TRUE 0.25 90.099999999999994 Positive NES GSEA lisa_lollipop 34 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 260 150 150 0 110 57.692307692307693 3.4768584828011973e-13 12 8 TRUE significant 102 48 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 8% 12/150 S1 · ≥8% · 12/150 Observed NES of both signs +102 / -48 / zero 0 / missing 0; N=150 TRUE hommel-support-ui-v1 CYTOSKELETON_CONTRACTILITY Cytoskeleton and contractility STRUCTURE_MOTILITY_PLASTICITY Structure, motility and plasticity 24 2 #BB7FE2 89 419 243 89 84 5 1.3313668389522899 0.80358233769611598 1.51154755512412 -1.69566919273452 1.4176174002709701 0.94382022471910099 1.6566767311418501e-12 1.6566767311418501e-12 TRUE 0.25 94.400000000000006 Positive NES GSEA lisa_lollipop 35 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 419 243 243 0 176 57.995226730310264 1.6942845267835841e-09 6 2.4691358024691357 TRUE significant 198 45 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 2.46% 6/243 S1 · ≥2.46% · 6/243 Observed NES of both signs +198 / -45 / zero 0 / missing 0; N=243 TRUE hommel-support-ui-v1 EMT_PLASTICITY EMT and cell-state plasticity STRUCTURE_MOTILITY_PLASTICITY Structure, motility and plasticity 24 3 #AB6DD2 0 34 11 0 0 0 0.63603712987804195 0.71666676083234904 FALSE 0.25 GSEA lisa_lollipop 36 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 34 11 11 0 23 32.352941176470587 1 0 0 FALSE not_significant 10 1 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 No minimum greater than zero could be supported 0% 0/11 Observed NES of both signs +10 / -1 / zero 0 / missing 0; N=11 FALSE hommel-support-ui-v1 MIGRATION_INVASION Migration, invasion and motility programs STRUCTURE_MOTILITY_PLASTICITY Structure, motility and plasticity 24 4 #9560B8 49 215 100 49 46 3 1.5013246743637501 1.0883608693098299 1.6914194896008701 -1.4134624926053301 1.70028144729876 0.93877551020408201 2.2713362499723099e-07 2.2713362499723099e-07 TRUE 0.25 93.900000000000006 Positive NES GSEA lisa_lollipop 37 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 215 100 100 0 115 46.511627906976742 0.00057577643409300802 4 4 TRUE significant 87 13 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 4% 4/100 S1 · ≥4% · 4/100 Observed NES of both signs +87 / -13 / zero 0 / missing 0; N=100 TRUE hommel-support-ui-v1 ION_TRANSPORT_HOMEOSTASIS Ion transport and homeostasis TRANSPORT_TRAFFICKING_HOMEOSTASIS Transport, trafficking and homeostasis 25 1 #E486CC 56 382 133 56 10 46 -1.1427775221523699 -0.518309662858362 1.5123365191981999 -1.7199762267937899 -1.5368866148517499 0.82142857142857095 1.4522377895813199e-28 1.4522377895813199e-28 TRUE 0.25 82.099999999999994 Negative NES GSEA lisa_lollipop 38 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 382 133 133 0 249 34.816753926701573 4.2206814392778386e-26 6 4.511278195488722 TRUE significant 45 88 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 4.51% 6/133 S1 · ≥4.51% · 6/133 Observed NES of both signs +45 / -88 / zero 0 / missing 0; N=133 TRUE hommel-support-ui-v1 TRANSPORT_LOCALIZATION Transport and localization TRANSPORT_TRAFFICKING_HOMEOSTASIS Transport, trafficking and homeostasis 25 2 #DD64BE 86 418 199 86 36 50 -0.30470918704075201 -0.10606258747908801 1.6296070289278899 -1.69741686253818 -1.38765144443148 0.581395348837209 2.8199520185886402e-19 2.8199520185886402e-19 TRUE 0.25 58.100000000000001 Negative NES GSEA lisa_lollipop 39 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 418 199 199 0 219 47.607655502392348 1.3308449953466171e-16 6 3.0150753768844223 TRUE significant 96 103 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 3.01% 6/199 S1 · ≥3.01% · 6/199 Observed NES of both signs +96 / -103 / zero 0 / missing 0; N=199 TRUE hommel-support-ui-v1 VESICLE_SECRETORY_TRAFFICKING Vesicle, endocytosis, exocytosis and secretion TRANSPORT_TRAFFICKING_HOMEOSTASIS Transport, trafficking and homeostasis 25 3 #B5529C 59 373 228 59 37 22 0.36365435740517299 0.202084013657681 1.5503828384215499 -1.63220717884964 1.36079512114975 0.62711864406779705 4.7145495415061699e-07 4.7145495415061699e-07 TRUE 0.25 62.700000000000003 Positive NES GSEA lisa_lollipop 40 TRUE TRUE supracategory hommel_support_v1 ccRCC tumour minus NAT Paired tumour minus NAT abundance Positive values indicate higher tumour abundance. 13 15.600000000000001 300 white cptac_ccrcc_tumor_minus_nat GOBP-C2 373 228 228 0 145 61.126005361930297 0.001273674028848915 2 0.8771929824561403 TRUE significant 131 97 0 0 0.050000000000000003 0.94999999999999996 6673 All eligible unique gene-set nulls across configured LISA category collections within one DE analysis; HALLMARKS excluded hommel::hommel(simes=FALSE); invert localtest partial-conjunction tests cptac_ccrcc_tumor_minus_nat:1427191c6936f29d support-grades-v1 S1 Enrichment supported; minimum below 10% 0.87% 2/228 S1 · ≥0.87% · 2/228 Observed NES of both signs +131 / -97 / zero 0 / missing 0; N=228 TRUE hommel-support-ui-v1