Table 4 Reactome pathways enriched with genes involved in the top 1% subnetworks obtained when considering binary and co-complex interactions.
Interactions type | Enriched reactome pathway | Genes (N) | PEMPa | PFDRb |
|---|---|---|---|---|
Binary | Striated muscle contraction | 7 | 2.2 × 10–10 | 7.3 × 10–08 |
Muscle contraction | 9 | 3.6 × 10–07 | 5.9 × 10–05 | |
Glycogen breakdown (glycogenolysis) | 3 | 7.3 × 10–05 | 7.9 × 10–03 | |
Glycogen metabolism | 3 | 3.2 × 10–04 | 2.5 × 10–02 | |
The role of GTSE1 in G2/M progression after G2 checkpoint | 4 | 3.9 × 10–04 | 2.5 × 10–02 | |
Co-complex | Peptide chain elongation | 37 | 4.4 × 10–53 | 1.2 × 10–50 |
Viral mRNA translation | 37 | 4.4 × 10–53 | 1.2 × 10–50 | |
Formation of a pool of free 40S subunits | 38 | 1.6 × 10–52 | 3.0 × 10–50 | |
Eukaryotic translation elongation | 37 | 3.4 × 10–52 | 3.1 × 10–50 | |
Selenocysteine synthesis | 37 | 3.4 × 10–52 | 3.1 × 10–50 | |
Eukaryotic translation termination | 37 | 3.4 × 10–52 | 3.1 × 10–50 | |
Nonsense mediated decay (NMD) independent of the exon junction complex (EJC) | 37 | 9.1 × 10–52 | 7.2 × 10–50 | |
L13a-mediated translational silencing of ceruloplasmin expression | 38 | 1.3 × 10–50 | 8.7 × 10–49 | |
GTP hydrolysis and joining of the 60S ribosomal subunit | 38 | 1.9 × 10–50 | 1.2 × 10–48 | |
Nonsense-mediated decay (NMD) | 38 | 6.3 × 10–50 | 3.1 × 10–48 | |
Nonsense mediated decay (NMD) enhanced by the exon junction complex (EJC) | 38 | 6.3 × 10–50 | 3.1 × 10–48 | |
Eukaryotic translation initiation | 38 | 2.9 × 10–49 | 1.2 × 10–47 | |
Cap-dependent translation initiation | 38 | 2.9 × 10–49 | 1.2 × 10–47 | |
SRP-dependent cotranslational protein targeting to membrane | 37 | 1.5 × 10–48 | 5.9 × 10–47 | |
Selenoamino acid metabolism | 37 | 1.5 × 10–47 | 5.3 × 10–46 | |
Influenza viral RNA transcription and replication | 38 | 4.0 × 10–47 | 1.4 × 10–45 | |
Major pathway of rRNA processing in the nucleolus and cytosol | 41 | 5.8 × 10–47 | 1.9 × 10–44 | |
Regulation of expression of SLITs and ROBOs | 40 | 8.3 × 10–46 | 2.5 × 10–44 | |
Influenza life cycle | 38 | 9.3 × 10–46 | 2.7 × 10–44 | |
rRNA processing in the nucleus and cytosol | 41 | 6.2 × 10–45 | 1.7 × 10–43 | |
Influenza Infection | 38 | 2.2 × 10–44 | 5.8 × 10–43 | |
rRNA processing | 41 | 5.8 × 10–44 | 1.5 × 10–42 | |
Signaling by ROBO receptors | 40 | 3.2 × 10–41 | 7.8 × 10–40 | |
Translation | 40 | 5.9 × 10–36 | 1.6 × 10–34 | |
Infectious disease | 41 | 1.9 × 10–32 | 4.2 × 10–31 | |
Metabolism of amino acids and derivatives | 39 | 1.9 × 10–30 | 4.1 × 10–29 | |
Formation of the ternary complex, and subsequently, the 43S complex | 19 | 5.1 × 10–26 | 1.0 × 10–24 | |
Translation initiation complex formation | 19 | 9.4 × 10–25 | 1.8 × 10–23 | |
Ribosomal scanning and start codon recognition | 19 | 9.4 × 10–25 | 1.8 × 10–23 | |
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 19 | 1.4 × 10–24 | 2.5 × 10–23 | |
TCR signaling | 6 | 1.1 × 10–3 | 2.0 × 10–2 | |
Regulation of mRNA stability by proteins that bind AU-rich elements | 5 | 1.7 × 10–3 | 3.0 × 10–2 | |
FBXL7 down-regulates AURKA during mitotic entry and in early mitosis | 4 | 1.9 × 10–3 | 3.2 × 10–2 | |
Insulin receptor recycling | 3 | 2.1 × 10–3 | 3.3 × 10–2 | |
Regulation of RUNX3 expression and activity | 4 | 2.1 × 10–3 | 3.3 × 10–2 | |
Insulin processing | 3 | 2.3 × 10–3 | 3.5 × 10–2 | |
Stabilization of p53 | 4 | 2.4 × 10–3 | 3.5 × 10–2 | |
Iron uptake and transport | 4 | 2.5 × 10–3 | 3.7 × 10–2 | |
Downstream TCR signaling | 5 | 2.8 × 10–3 | 3.9 × 10–2 | |
G2/M transition | 7 | 3.0 × 10–3 | 4.2 × 10–2 | |
Mitotic G2-G2/M phases | 7 | 3.2 × 10–3 | 4.2 × 10–2 | |
rRNA modification in the nucleus and cytosol | 4 | 3.2 × 10–3 | 4.2 × 10–2 | |
Transferrin endocytosis and recycling | 3 | 3.4 × 10–3 | 4.4 × 10–2 | |
Cilium assembly | 7 | 3.5 × 10–3 | 4.4 × 10–2 | |
ROS, RNS production in phagocytes | 3 | 3.8 × 10–3 | 4.6 × 10–2 | |
p53-dependent G1 DNA damage response | 4 | 4.0 × 10–3 | 4.7 × 10–2 | |
p53-dependent G1/S DNA damage checkpoint | 4 | 4.0 × 10–3 | 4.7 × 10–2 |
