Table 4 Pathways enriched for ACE-associated modules

LightCyan1 (48)

–

–

–

–

–

–

Blue (109,576)

7.28 × 10^–10

hsa05014

Amyotrophic lateral sclerosis

9.79 × 10^–158

GO:0043231 (CC)

Intracellular membrane-bounded organelle

9.98 × 10^–09

hsa05016

Huntington disease

4.50 × 10^–150

GO:0043229 (CC)

Intracellular organelle

9.98 × 10^–09

hsa05022

Pathways of neurodegeneration—multiple diseases

2.35 × 10^–138

GO:0005622 (CC)

Intracellular anatomical structure

1.20 × 10^–07

hsa03040

Spliceosome

9.12 × 10^–120

GO:0005654 (CC)

Nucleoplasm

1.20 × 10^–07

hsa04144

Endocytosis

2.50 × 10^–116

GO:0043227 (CC)

Membrane-bounded organelle

1.20 × 10^–07

hsa04390

Hippo signaling pathway

5.08 × 10^–114

GO:0043226 (CC)

Organelle

1.46 × 10^–07

hsa03010

Ribosome

7.24 × 10^–102

GO:0005634 (CC)

Nucleus

2.96 × 10^–07

hsa05165

Human papillomavirus infection

3.06 × 10^–100

GO:0044260 (BP)

Cellular macromolecule metabolic process

5.62 × 10^–07

hsa05168

Herpes simplex virus 1 infection

4.11 × 10^–90

GO:0044237 (BP)

Cellular metabolic process

1.65 × 10^–06

hsa04110

Cell cycle

2.83 × 10^–89

GO:0005515 (MF)

Protein binding

Pink (12,955)

0.028

hsa05020

Prion disease

4.95 × 10^–23

GO:0005654 (CC)

Nucleoplasm

0.040

hsa03010

Ribosome

3.96 × 10^–19

GO:0003676 (MF)

Nucleic acid binding

0.040

hsa03050

Proteasome

5.67 × 10^–19

GO:0034641 (BP)

Cellular nitrogen compound metabolic process

1.52 × 10^–18

GO:0006139 (BP)

Nucleobase-containing compound metabolic process

1.52 × 10^–18

GO:0044271 (BP)

Cellular nitrogen compound biosynthetic process

2.30 × 10^–18

GO:0070013 (CC)

Intracellular organelle lumen

2.71 × 10^–18

GO:0031981 (CC)

Nuclear lumen

2.71 × 10^–18

GO:0034645 (BP)

Cellular macromolecule biosynthetic process

5.37 × 10^–18

GO:0009059 (BP)

Macromolecule biosynthetic process

5.37 × 10^–18

GO:0031974 (CC)

Membrane-enclosed lumen

SkyBlue4 (63)

–

–

–

–

–

–

Salmon (2531)

1.03 × 10^–7

hsa04659

Th17 cell differentiation

3.75 × 10^–22

GO:0001775 (BP)

Lymphocyte activation

2.14 × 10^–7

hsa04060

Cytokine–cytokine receptor interaction

3.75 × 10^–22

GO:0046649 (BP)

T cell activation

1.01 × 10^–6

hsa04660

T cell receptor signaling pathway

5.89 × 10^–22

GO:0042110 (BP)

Leukocyte activation

2.21 × 10^–5

hsa04658

Th1 and Th2 cell differentiation

7.57 × 10^–22

GO:0045321 (BP)

Immune system process

5.19 × 10^–5

hsa04640

Hematopoietic cell lineage

8.86 × 10^–21

GO:0002376 (BP)

Immune response

1.4 × 10^–4

hsa05166

Human T-cell leukemia virus 1 infection

8.06 × 10^–19

GO:0006955 (BP)

adaptive immune response

1.4 × 10^–4

hsa05235

PD-L1 expression and PD-1 checkpoint pathway in cancer

2.33 × 10^–15

GO:0002250 (BP)

T cell differentiation

0.001

hsa04061

Viral protein interaction with cytokine and cytokine receptor

2.63 × 10^–13

GO:0030217 (BP)

Immune effector process

0.003

hsa04064

NF-kappa B signaling pathway

3.64 × 10^–13

GO:0002252 (BP)

Regulation of immune system process

0.003

hsa05170

Human immunodeficiency virus 1 infection

1.49 × 10^–12

GO:0002682 (BP)

Lymphocyte differentiation

SaddleBrown (94)

–

–

–

0.003

GO:0048704 (BP)

Embryonic skeletal system morphogenesis

0.003

GO:0048706 (BP)

Embryonic skeletal system development

0.007

GO:0009952 (BP)

Anterior/posterior pattern specification

0.011

GO:0048705 (BP)

Skeletal system morphogenesis

0.020

GO:0048652 (BP)

Embryonic organ morphogenesis

0.024

GO:0003002 (BP)

Regionalization

0.047

GO:0007389 (BP)

Pattern specification process

0.047

GO:0048568 (BP)

Embryonic organ development

RoyalBlue (296)

–

–

–

–

–

–

Magenta (3363)

–

–

–

7.45 × 10^–6

GO:0002376 (BP)

Immune system process

4.76 × 10^–5

GO:0006955 (BP)

Immune response

0.004

GO:0006954 (BP)

Inflammatory response

0.006

GO:0001775 (BP)

Cell activation

0.03

GO:0002366 (BP)

Leukocyte activation involved in immune response

0.03

GO:0006887 (BP)

Exocytosis

0.03

GO:0030097 (BP)

Hemopoiesis

0.03

GO:0045055 (BP)

Regulated exocytosis

0.03

GO:0048534 (BP)

Hematopoietic or lymphoid organ development

0.032

GO:0045321 (BP)

Leukocyte activation

MidnightBlue (822)

1.69 × 10^–7

hsa04650

Natural killer cell-mediated cytotoxicity

0.008

GO:0002682 (BP)

Regulation of immune system process

0.016

hsa04660

T cell receptor signaling pathway

0.013

GO:0035556 (BP)

Intracellular signal transduction

0.016

hsa05135

Yersinia infection

0.019

GO:0006955 (BP)

Immune response

0.040

hsa05332

Graft-versus-host disease

0.022

GO:0002228 (BP)

Natural killer cell-mediated immunity

0.033

GO:0050776 (BP)

Regulation of immune response

0.038

GO:0001906 (BP)

Cell killing

0.038

GO:0006952 (BP)

Defense response

0.038

GO:0007159 (BP)

Leukocyte cell–cell adhesion

0.039

GO:0006909 (BP)

Phagocytosis

0.039

GO:0046649 (BP)

Lymphocyte activation

Brown (91,675)

0.032

hsa04012

ErbB signaling pathway

0.002

GO:0042995 (CC)

Cell projection

0.032

hsa04921

Oxytocin signaling pathway

0.002

GO:0043167 (MF)

Ion binding

0.009

GO:0120025 (CC)

Plasma membrane-bounded cell projection

0.030

GO:0046873 (MF)

Metal ion transmembrane transporter activity

Turquoise (84,323)

0.001

hsa04020

Calcium signaling pathway

9.94 × 10^–42

GO:0071944 (CC)

Cell periphery

0.001

hsa04072

Phospholipase D signaling pathway

2.58 × 10^–32

GO:0005886 (CC)

Plasma membrane

0.001

hsa05150

Staphylococcus aureus infection

3.41 × 10^–19

GO:0031224 (CC)

Intrinsic component of membrane

0.001

hsa05414

Dilated cardiomyopathy

1.06 × 10^–15

GO:0016021 (CC)

Integral component of membrane

0.003

hsa05410

Hypertrophic cardiomyopathy

6.08 × 10^–14

GO:0005261 (MF)

Cation channel activity

0.007

hsa04060

Cytokine–cytokine receptor interaction

1.70 × 10^–13

GO:0046873 (MF)

Metal ion transmembrane transporter activity

0.007

hsa04080

Neuroactive ligand-receptor interaction

2.07 × 10^–13

GO:0015267 (MF)

Channel activity

0.007

hsa04261

Adrenergic signaling in cardiomyocytes

3.39 × 10^–13

GO:0022803 (MF)

Passive transmembrane transporter activity

0.007

hsa04512

ECM-receptor interaction

5.09 × 10^–13

GO:0031226 (CC)

Intrinsic component of plasma membrane

0.007

hsa04975

Fat digestion and absorption

3.09 × 10^–12

GO:0005216 (MF)

Ion channel activity

Ivory (85)

–

–

–

5.91 × 10^–28

GO:0007156 (BP)

Homophilic cell adhesion via plasma membrane adhesion molecules

2.00 × 10^–24

GO:0098742 (BP)

Cell–cell adhesion via plasma-membrane adhesion molecules

1.50 × 10^–17

GO:0005509 (MF)

Calcium ion binding

5.37 × 10^–16

GO:0098609 (BP)

Cell–cell adhesion

2.27 × 10^–12

GO:0007155 (BP)

Cell adhesion

2.27 × 10^–12

GO:0022610 (BP)

Biological adhesion

1.13 × 10^–11

GO:0005887 (CC)

Integral component of plasma membrane

2.18 × 10^–11

GO:0031226 (CC)

Intrinsic component of plasma membrane

3.51 × 10^–04

GO:0046872 (MF)

Metal ion binding

4.25 × 10^–04

GO:0043169 (MF)

Cation binding

Sienna4 (33)

–

–

–

–

–

–

DarkOliveGreen (72)

–

–

–

–

–

–

Yellow3 (59)

–

–

–

–

–

–