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Table 3 Pathway Enrichment analysis

From: Evaluation of copy number variation and gene expression in neurofibromatosis type-1-associated malignant peripheral nerve sheath tumours

  Pathway name P value Genes Fold change (3 benign vs. 3 malignant) Fold change (4 benign vs. 5 malignant
1 Glutathione metabolism 0.00056 GSTM1 −3.25 −2.27
GSTM2 −3.25 −2.27
GSTM4 −3.25 −2.27
2 Glutathione metabolism/human version 0.00059 GSTM1 −3.25 −2.27
GSTM2 −3.25 −2.27
GSTM4 −3.25 −2.27
3 Glutathione metabolism/rodent version 0.00073 GSTM1 −3.25 −2.27
GSTM2 −3.25 −2.27
GSTM4 −3.25 −2.27
4 Development: Wnt signalling pathway. Degradation of beta-catenin in the absence Wnt signalling 0.00106 CSNK1D 2.42 1.99
DAB2 3.46 2.65
5 Cell adhesion: PLAU signalling 0.00445 HGF 7.80 10.97
SERPINE1 5.74 4.54
6 Role of alpha-6/beta-4 integrins in carcinoma progression 0.00589 HGF 7.80 10.97
LIMK1 2.04 2.23
7 Development: TGF-beta-dependent induction of EMT via MAPK 0.00641 DAB2 3.46 2.65
SERPINE1 5.74 4.54
8 Transport: macropinocytosis regulation by growth factors 0.01130 HGF 7.80 10.97
LIMK1 2.04 2.23
9 Development: regulation of epithelial-to-mesenchymal transition (EMT) 0.01165 HGF 7.80 10.97
SERPINE1 5.74 4.54
10 Transport: clathrin-coated vesicle cycle 0.01421 PREB 1.45 1.43
DAB2 3.46 2.65
  1. The pathways were ranked by hypergeometric P values, and a summary of the top ten pathways is reported. The P value represents the probability that a gene set of this size would co-occur by chance alone. Network objects represent the ratio of the number of genes from the list compared to the total number of genes known to be associated with the pathway.