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Table 3 The significant GO-terms GO-id and KEGG pathways found in the bicliques extracted from HV _ negative 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 env_gp120 env_gp160 env_gp41 MAN1B1 MGAT2 MAN2C1 MAN2A1 MAN2A2 MANBA GBA3 MAN2B2 GAA MAN2B1 MAN1A1 MAN1A2 MAN1C1 GCS1 GANAB GANC GBA2 Mannose metabolic process (GO:0006013) (4.5E-11) Golgi apparatus part (GO:0044431) (6.9E-6) Mannosidase activity (GO:0015923) (8.7E-25) N-Glycan biosynthesis (1.0E-11)
2 Rev capsid matrixnucleocapsid p1 p6 UBB UBC UBD Long-term strengthening of neuromuscular junction (GO:0042062) (7.4E-4) Cytosolic small ribosomal subunit (GO:0022627) (3.1E-3) Structural constituent of ribosome (GO:0003735) (1.3E-2) Not found
3 Rev Tat matrix p6 MAPK1 MAPK3 UBB UBC UBD Cell cycle (GO:0007049)(7.2E-4) Nucleoplasm (3.3E-4) MAP kinase activity (GO:0004707) (3.2E-3) Dorso-ventral axisformation (1.5E-2)
4 RT Vif env_gp120 IFNA1 IFNA16 IFNA2 IFNA7 Response to virus (GO:0009615) (5.1E-7) Extracellular space (GO:0005615) (1.5E-4) Interferon-alpha/beta receptor binding (GO:0005132) (2.3E-10) Regulation of autophagy (3.0E-7)
5 Rev Vpu matrix retropepsin CSNK2A1 CSNK2A2 CSNK2B Wnt receptor signaling pathway (GO:0016055) (GO:0016055) (9.6E-5) Not found Protein serine/threoninekinase activity (Adherensjunction (2.3E-4)  
6 Rev Tat Vif matrix p6 MAPK1 MAPK3 Ras protein signaltransduction (GO:0007265) (7.8E-3) Nucleolus (GO:0005730)(5.5E-2) MAP kinase activity (GO:0004707) (1.1E-3) Dorso-ventral axis formation (4.9E-3)
7 RT Rev Vpu matrix retropepsin CSNK2A1 CSNK2B Wnt receptor signaling pathway (GO:0016055) (9.8E-3) Not found Protein serine/threonine kinase activity (GO:0004674) (3.3E-2) Adherens junction (1.5E-2)
8 RT Rev matrix CSNK2A1 CSNK2B PRKCA Wnt receptor signaling pathway (GO:0016055) (2.0E-2) Not found Protein serine/threonine kinase activity (GO:0004674) (1.1E-3) Tight junction junction (6.9E-4)
9 Tat integrase matrix KPNB1 RANBP5 TNPO1 Protein import into nucleus, docking (GO:0000059) (1.3E-3) Nuclear pore (GO:0005643) (6.2E-3) Nuclear localization sequence binding (GO:0008139) (5.4E-4) Not found
10 Rev Tat matrix MAPK1 MAPK3 PRKCA UBB UBC UBD Regulation ofsynaptogenesis(GO:0051963) (1.7E-5) Cytosol (GO:0005829)(1.2E-4) MAP kinase activity (GO:0004707) (4.3E-3) Aldosterone-regulated sodium reabsorption (6.3E-5)
11 Nef env_gp120 env_gp160 CD4 ITGAL ICAM1 HLA-DRB1 PRKCQ LCK T cell activation (GO:0006468) (7.8E-6) Plasma membrane part (GO:0044459) (1.5E-4) Glycoprotein binding (GO:0001948) (1.4E-2) Cell adhesion molecules (CAMs) (1.6E-4)
12 Tat capsid env_gp120 IFNG CD3D CD3E CD3G T cell activation (GO:0042110) (2.6E-4) Alpha-beta T cell recep- tor complex (GO:0042105) (2.2E-7) T cell receptor binding (GO:0042608) (6.9E-4) T cell receptor signaling pathway (9.3E-6)
13 Nef env_gp120 env_gp41 CXCR4 CD4 Initiation of viral infection (GO:0019059) (1.6E-3) Not found Coreceptor activity (GO:0015026) (1.5E-3) Not found
14 Nef Tat env_gp120 TP53 ICAM1 T cell activation during immune response (GO:0002286) (9.6E-4) Not found Not found Not found
15 Nef Tat Vpr CDK9 TP53 Transcription,DNA-dependent(GO:0006351) (2.2E-2) Nucleoplasm part (GO:0044451) (4.3E-2) Not found Not found
16 Nef RT Tat PRKCA TP53 Induction of apoptosis by intracellular signals (GO:0008629) (4.0E-3) Nsoluble fraction (GO:0005626) (6.6E-2) Not found Non-small cell lung cancer (1.1E-2)
17 Tat env_gp120 env_gp160 CD28 ICAM1 Regulation of immune effector process (GO:0002697) (7.5E-3) External side of plasma membrane (GO:0009897) (1.3E-2)   Viral myocarditis (1.4E2)
18 Tat Vpr env_gp120 TP53 NFKB1 Regulation of specific transcription from RNA polymerase II promote(GO:0006357)(6.9E-3) Nucleoplasm (GO:0005654) (3.3E-4) Promoter binding (GO:0010843) (4.4E-3) Pancreatic cancer (1.4E-2)
19 Tat env_gp120 env_gp41 CCL5 IFNG Leukocyte chemotaxis (GO:0030595) (2.7E-3) Extracellular space (GO:0005615) (5.4E-2) Cytokine activity (GO:0005125) (1.5E-2) Cytokine-cytokinereceptor interaction (5.2E-2)