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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

From: Incorporating the type and direction information in predicting novel regulatory interactions between HIV-1 and human proteins using a biclustering approach

Biclique HIV protein Human protein GO term (bp) GO term (cc) GO term (mf) KEGG pathway
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