Table 4 Literature references for predicted FIs added to human curated GBM pathway from the TCGA GBM data set
From: A human functional protein interaction network and its application to cancer data analysis
Pathway gene | FI partner | Reference | Comment |
|---|---|---|---|
CCNE1 | FBXW7 | [99] | Turnover of CCNE1 protein is dependent on FBXW7 protein |
CDK4 | ASPM | [100] | Physical interaction: functional relationship is not clear |
CDKN1A | PIM1 | [101] | Pim-1 kinase dependent phosphorylation of p21Cip1/WAF1 (CDKN1A) influences subcellular localization of p21 |
CDKN1B | NUP50 | [70] | NUP50 protein is required for degradation of CDKN1B protein, which is important in cell cycle regulation |
E2F1 | TRRAP | [102] | TRRAP is required as a cofactor for E2F transcriptional activation |
EGFR | ANXA1 | [103] | ANXA1 protein and other annexins are involved in degradation of EGFR protein |
EGFR | ROS1 | Â | This may be a false positive example |
EGFR | TNC | [71] | TNC protein is a ligand for EGFR |
EP300 | GLI1 | [104] | GLI1 is involved in a GLU1-p53 inhibitory loop |
EP300 | IQGAP1 | [105] | Physical interaction: functional relationship is not clear |
EP300 | PROX1 | [106] | Physical interaction: functional relationship is not clear |
EP300 | TCF12 | [107] | Form a functional complex in neurons |
GRB2 | SYP | [108] | SYP involvement in the RAS pathway has been reported some time ago |
GRB2 | TNK2 | [109] | TNK2 protein is a target of GRB2 protein |
MSH6 | PMS2 | [110] | PMS2 has been treated as a DNA repair gene |
PDPK1 | RPS6KA3 | [111] | Phosphoserine-mediated recruitment of PDPK1 to RPS6KA3 leads to coordinated phosphorylation and activation of PDPK1 and RPS6KA3 |
PRKCA | ANXA7 | [112] | Calcium-dependent membrane fusion driven by annexin 7 can be potentiated by protein kinase C and guanosine triphosphate |
SRC | CD46 | [113] | CD46 is a substrate of SRC |
SRC | MAPK8IP2 | [114] | Though no direct evidence shows a functional relationship between these two genes, it is shown that an isoform of JIP (MAPK8IP2), JIP1, is regulated by Src family kinases |
TP53 | CYLD | Â | CYLD is a deubiquitinating enzyme. Several deubiquitinating enzyme have been shown to be involved in the p53 pathway; however, no evidence has been provided for CYLD in the p53 pathway |
TP53 | KLF4 | [115] | KLF4 is a direct suppressor of expression of TP53 |
TP53 | KLF6 | [116] | Physical interaction: TP53 may enhance the function of KLF6 |
TP53 | TOP1 | [117] | Activity of TOP1 may be modulated by P53 |