Table 2 The significant GO-terms, GO-id and KEGG pathways found in the bicliques extracted from HV _ positive matrix, considering interaction types and direction of the interactions

1

Tat Vpr env_gp120 matrix

BCL2 CASP3 TP53 IFNG IFNG IL10 IL2 IL6 MAPK1 NFKB1 PARP1 FOS JUN TNF

Regulation of apoptosis (GO: 0042981) (3.1E-11)

Nucleoplasm (GO:0005654) (6.8E-5)

Promoter binding (GO:0010843) (1.7E-5)

T cell receptor signaling pathway (1.2E-9)

2

Nef Tat env_gp120env_gp160

BCL2 ICAM1 IFNG IL1B IL2 IL6 MAPK1 MAPK3 FOS JUN

Positive regulation of nitrogen compound metabolic process (GO: 0051173) (1.8E-8)

Extracellular space (GO:0005615) (8.3E-4)

Cytokine activity (GO:0005125) (2.6E-4)

Toll-like receptor signaling pathway (3.3E-7)

3

Nef Vpr env_gp120env_gp160

CD4 BCL2 IFNG IL2 IL6 MAPK14 MAPK1 FOS JUN

Positive regulation of macromolecule metabolic process (GO:0010604) (2.5E-10)

Nucleoplasm (GO:0005654) (1.4E-2)

Protein dimerizationactivity (GO:0046983)(3.5E-3)

T cell receptor signaling pathway (2.2E-9)

4

Nef Tat Vpr env_gp120env_gp160

BCL2 IFNG IL2 IL6 MAPK1 FOS JUN

Positive regulation of macromolecule metabolic process (GO:0010604) (6.4E-8)

Extracellular space (GO:0005615) (3.7E-2)

Cytokine activity (GO:0005125) (3.2E-3)

T cell receptor signalingpathway (2.8E-6)

5

Tat Vpr env_gp120env_gp160

BCL2 CYCS IFNG IL2 IL6 MAPK1 FOS JUN

Regulation of apoptosis (GO:0042981) (2.9E-7)

Protein phosphatase type 2A complex (GO:0000159) (1.1E-2)

Cytokine activity (GO:0005125) (4.5E-3)

Colorectal cancer (2.3E-6)

6

Nef Tat env_gp120env_gp41

CCL5 IFNG IL1B IL10 IL2 IL2RA IL6 TNF

Leukocyte migration (GO:0050900) (2.3E-11)

Extracellular space (GO:0005615) (1.6E-7)

Cytokine activity(GO:0005125) (7.4E-11)

Cytokine-cytokinereceptor interaction (8.9E-10)

7

Nef Tat Vpr env_gp120env_gp41

IFNG IL10 IL2 IL6 TNF

Regulation of immunoglobulinproduction (GO:0002637) (1.1E-11)

Extracellular space (GO:0005615) (8.2E-6)

Cytokine activity (GO:0005125) (4.9E-8)

Allograft rejection (1.3E-6)

8

Tat env_gp120 env_gp160 env_gp41

IL1A IL1B IL2 IL6 LCK

Positive regulation of protein transport (GO:0051222) (4.6E-7)

Extracellular space (GO:0005615) (5.9E-4)

Cytokine activity (GO:0005125) (1.3E-5)

Graft-versus-host disease(1.7E-6)

9

Nef Tat env_gp120 matrix

CCL3 IFNG IL6 TNF

Positive regulation of protein aminoacid phosphorylation(GO:0001934) (1.8E-9)

Extracellular space (GO:0005615) (8.2E-6)

Cytokine activity (GO:0005125) (4.9E-8)

Allograft rejection (1.3E-6)

10

Nef Tat Vpr env_gp120 env_gp41 matrix

IFNG IL6 TNF

Regulation of chemokine biosynthetic process (GO:0045073) (4.9E-7)

Extracellular space (GO:0005615) (2.9E-3)

Cytokine activity (GO:0005125) (2.2E-4)

Graft-versus-host disease(5.7E-5)

11

Tat Vpr env_gp120 retropepsin

BCL2 CASP3 CYCS PARP1

B cell homeostasis (GO:0001782) (2.4E-3)

Protein phosphatase type 2A complex (GO:0000159) (4.7E-3)

not found

Amyotrophic lateralsclerosis (ALS) (3.2E-4)

12

Tat Vpr env_gp120 matrix

CCL3 IFNG IL6 TNF

Regulation of chemokine biosynthetic process (GO:0045073) (1.5E-6)

Extracellular space (GO:0005615) (1.5E-4)

Cytokine activity (GO:0005125) (3.3E-6)

Cytokine-cytokine receptor interaction (1.4E-4)

13

Nef env_gp120 env_gp160 env_gp41

CD4 IL1B IL2 IL6

Positive regulation of T cell activation (activation(GO:0050870) (1.7E-7)

Extracellular space (GO:0005615) (8.3E-3) activity (GO:0008083) (4.5E-4)

Graft-versus-hostdisease (1.7E-4)

14

Nef Tat Vpr env_gp120 retropepsin

BCL2 CASP3 PARP1

B cell homeostasis (GO:0050870) (1.7E-7)

Nuclear envelope (GO:0005635) (3.2E-2)

Transcription factorbinding (GO:0008134)(7.7E-2)

Amyotrophic lateralsclerosis (ALS) (2.1E-2)

15

Nef Tat env_gp120 env_gp160 env_gp41

IL1B IL2 IL6

Positive regulation of immunoglobulinsecretion (GO:0051024)(3.7E-4)

Extracellular space (GO:0005615) (5.4E-2)

Not found

Not found

16

Nef Tat Vpr env_gp120 env_gp160 env_gp41

IL2 IL6

Positive regulation of immunoglobulin secretion secretion (GO:0051024) (3.7E-4)

Extracellular space (GO:0005615) (5.4E-2)

activity (GO:0008083)(1.2E-2)

Graft-versus-host disease (7.7E-3)

17

Nef Vpr Vpu env_gp120

CD4 CASP3 NFKB1

Regulation of T cellactivation (GO:0050863)(1.7E-2)

Intracellular organellelumen (GO:0070013)(1.9E-2)

Proteinhomodimerization activity(GO:0042803) (5.1E-2)

Epithelial cell signaling in Helicobacter pyloriinfection (2.7E-2)

18

Tat Vpr env_gp120 env_gp160 retropepsin

BCL2 CYCS

Positive regulation of catalytic activity activity (GO:0043085) (3.8E-2)

Protein phosphatase type 2A complex (GO:0000159)

Amyotrophic lateralsclerosis (ALS) (1.0E-2)

19

Nef env_gp160 env_gp41 matrix

CALM1 IL6

Positive regulation of DNA binding (GO:0043388) (5.2E-3)

Not found

Not found

Not found