Skip to main content

Table 1 Enrichment coefficients for top significance functional categories in different Consistency Tiers

From: Knowledge-based compact disease models identify new molecular players contributing to early-stage Alzheimer’s disease

Tier Go category TG CG ENR LOG10 (p) FDR
0 GO:0019894_kinesin_binding 8 4 15 −4.1 0.011
0 GO:0007269_neurotransmitter_secretion 38 7 5.7 −3.8 0.018
0 GO:0030426_growth_cone 30 6 6 −3.5 0.024
0 GO:0008021_synaptic_vesicle 42 7 5 −3.5 0.030
0 GO:0007204_elevation_of_cytosolic_calcium_ion_concentration 20 5 8 −3.5 0.028
0 GO:0051480_cytosolic_calcium_ion_homeostasis 22 5 7 −3.3 0.03
0 GO:0051279_regulation_of_release_of_sequestered_calcium_ion_into_cytosol 6 3 15 −3.2 0.05
0 GO:0030672_synaptic_vesicle_membrane 24 5 6.4 −3.1 0.06
0 GO:0010522_regulation_of_calcium_ion_transport_into_cytosol 7 3 13. −3.0 0.06
0 GO:0048854_brain_morphogenesis 7 3 13 −3.0 0.0
0 GO:0050852_T_cell_receptor_signaling_pathway 15 4 8 −3.0 0.06
0 GO:0051648_vesicle_localization 16 4 8 −2.9 0.06
0 GO:0051209_release_of_sequestered_calcium_ion_into_cytosol 8 3 12 −2.8 0.06
0 GO:0051282_regulation_of_sequestering_of_calcium_ion 8 3 12 −2.8 0.06
0 GO:0051283_negative_regulation_of_sequestering_of_calcium_ion 8 3 12 −2.8 0.06
0 GO:0002429_immune_response-activating_cell_surface_receptor_signaling_pathway 17 4 7 −2.7 0.06
0 GO:0002768_immune_response-regulating_cell_surface_receptor_signaling_pathway 17 4 7 −2.7 0.07
0 GO:0050851_antigen_receptor-mediated_signaling_pathway 17 4 7 −2.7 0.07
0 GO:0007281_germ_cell_development 29 5 5 −2.7 0.07
0 GO:0030594_neurotransmitter_receptor_activity 9 3 10 −2.6 0.08
1 GO:0060198_clathrin_sculpted_vesicle 5 3 19 −3.6 0.03
1 GO:0019894_kinesin_binding 9 5 18 −5.5 0.004
1 GO:0042288_MHC_class_I_protein_binding 6 3 16 −3.3 0.05
1 GO:0042287_MHC_protein_binding 7 3 14 −3.0 0.06
1 GO:0051279_regulation_of_release_of_sequestered_calcium_ion_into_cytosol 7 3 14 −3.0 0.06
1 GO:0005834_heterotrimeric_G-protein_complex 12 5 13 −4.8 0.0049
1 GO:0010524_positive_regulation_of_calcium_ion_transport_into_cytosol 5 2 13 −2.0 0.12
1 GO:0035267_NuA4_histone_acetyltransferase_complex 5 2 13 −2.0 0.12
1 GO:0043113_receptor_clustering 5 2 13 −2.0 0.12
1 GO:0045576_mast_cell_activation 5 2 13 −2.0 0.12
1 GO:0046173_polyol_biosynthetic_process 5 2 13 −2.0 0.12
1 GO:0051322_anaphase 5 2 13 −2.0 0.12
1 GO:0051668_localization_within_membrane 5 2 13 −2.0 0.12
1 GO:0010522_regulation_of_calcium_ion_transport_into_cytosol 8 3 12 −2.8 0.06
1 GO:0031177_phosphopantetheine_binding 8 3 12 −2.8 0.06
1 GO:0008277_regulation_of_G-protein_coupled_receptor_protein_signaling_pathway 12 4 11 −3.5 0.03
1 GO:0008298_intracellular_mRNA_localization 9 3 11 −2.7 0.07
1 GO:0032410_negative_regulation_of_transporter_activity 9 3 11 −2.7 0.07
1 GO:0010676_positive_regulation_of_cellular_carbohydrate_metabolic_process 6 2 11 −1.9 0.14
1 GO:0045298_tubulin_complex 6 2 11 −1.9 0.14
1+ 2 GO:0019894_kinesin_binding 9 6 12 −5.7 0.007
1+ 2 GO:0060198_clathrin_sculpted_vesicle 5 3 11 −2.8 0.06
1+ 2 GO:0008298_intracellular_mRNA_localization 9 5 10 −4.4 0.009
1+ 2 GO:0005871_kinesin_complex 8 4 9 −3.3 0.03
1+ 2 GO:0042288_MHC_class_I_protein_binding 6 3 9 −2.5 0.08
1+ 2 GO:0045298_tubulin_complex 6 3 9 −2.5 0.08
1+ 2 GO:0005834_heterotrimeric_G-protein_complex 12 5 7.5 −3.5 0.02
1+ 2 GO:0005881_cytoplasmic_microtubule 15 5 6 −3.0 0.04
1+ 2 GO:0008088_axon_cargo_transport 15 5 6 −3.0 0.04
1+ 2 GO:0008277_regulation_of_G-protein_coupled_receptor_protein_signaling_pathway 12 4 6 −2.5 0.08
1+ 2 GO:0014047_glutamate_secretion 12 4 6 −2.5 0.08
1+ 2 GO:0032182_small_conjugating_protein_binding 16 5 5.6 −2.9 0.045
1+ 2 GO:0043130_ubiquitin_binding 16 5 5.6 −2.9 0.045
1+ 2 GO:0006458_‘de_novo’_protein_folding 26 8 5.5 −4.3 0.009
1+ 2 GO:0006941_striated_muscle_contraction 13 4 5.5 −2.3 0.09
1+ 2 GO:0072384_organelle_transport_along_microtubule 13 4 5.5 −2.3 0.09
1+ 2 GO:0051084_‘de_novo’_posttranslational_protein_folding 24 7 5 −3.6 0.02
1+ 2 GO:0005876_spindle_microtubule 18 5 5 −2.6 0.07
1+ 2 GO:0005200_structural_constituent_of_cytoskeleton 33 9 5 −4.3 0.01
1+ 2 GO:0010970_microtubule-based_transport 26 7 5 −3.4 0.02
1+ 2+ 3 GO:0033180_proton-transporting_V-type_ATPase__V1_domain 7 6 6 −4.2 0.0018
1+ 2+ 3 GO:0004708_MAP_kinase_kinase_activity 6 5 6 −3.4 0.006
1+ 2+ 3 GO:0042288_MHC_class_I_protein_binding 6 5 6 −3.4 0.006
1+ 2+ 3 GO:0042777_plasma_membrane_ATP_synthesis_coupled_proton_transport 6 5 6 −3.4 0.006
1+ 2+ 3 GO:0030897_HOPS_complex 5 4 5 −2.7 0.025
1+ 2+ 3 GO:0031338_regulation_of_vesicle_fusion 5 4 5 −2.7 0.025
1+ 2+ 3 GO:0035542_regulation_of_SNARE_complex_assembly 5 4 5 −2.7 0.025
1+ 2+ 3 GO:0060198_clathrin_sculpted_vesicle 5 4 5 −2.7 0.025
1+ 2+ 3 GO:0046933_hydrogen_ion_transporting_ATP_synthase_activity__rotational_mechanism 15 11 5 −6.3 0
1+ 2+ 3 GO:0046961_proton-transporting_ATPase_activity__rotational_mechanism 18 13 5 −7.2 0
1+ 2+ 3 GO:0004712_protein_serine_threonine_tyrosine_kinase_activity 7 5 5 −2.9 0.014
1+ 2+ 3 GO:0042287_MHC_protein_binding 7 5 5 −2.9 0.014
1+ 2+ 3 GO:0033178_proton-transporting_two-sector_ATPase_complex__catalytic_domain 17 12 5 −6.5 0
1+ 2+ 3 GO:0019894_kinesin_binding 9 6 4.5 −3.2 0.008
1+ 2+ 3 GO:0010676_positive_regulation_of_cellular_carbohydrate_metabolic_process 6 4 4.5 −2.2 0.059
1+ 2+ 3 GO:0035493_SNARE_complex_assembly 6 4 4.5 −2.3 0.059
1+ 2+ 3 GO:0045261_proton-transporting_ATP_synthase_complex__catalytic_core_F(1) 6 4 4.5 −2.3 0.059
1+ 2+ 3 GO:0045739_positive_regulation_of_DNA_repair 6 4 4.5 −2.3 0.059
1+ 2+ 3 GO:0045913_positive_regulation_of_carbohydrate_metabolic_process 6 4 4.5 −2.3 0.059
1+ 2+ 3 GO:0009135_purine_nucleoside_diphosphate_metabolic_process 8 5 4 −2.6 0.032
  1. TG – total genes in a given functional category within the total list T, CG – changed genes within the list L, ENR – enrichment coefficient, LOG10(p) – logarithm of p-value of one-sided Fisher’s test of significance of a given ENR at a given group size, FDR – false discovery rate. Venn Tier 1 + 2 is the combination of the Tier 1 and Tier 2, Venn Tier 1+ 2 + 3 is the combination of the Tiers 1, 2 and 3.