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.