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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   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   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