Table 4.

Biological pathways enriched in differentially expressed genes in ulcerated tumors using test and Leeds replication datasets.

Pathway		Test set (92 ulcerated, 256 not ulcerated)		Leeds replication (68 ulcerated, 56 not ulcerated)
		Fold enrichment	BH - FDR	Fold enrichment	BH - FDR
Regulation of cell proliferation	GO - BP	2.52	8.6×10−4	1.54	0.10
Pathways in cancer	KEGG	11.23	8.9×10−17	2.17	0.003
Cell cycle process	GO - BP	2.93	0.03	1.58	0.06
Plasma membrane part	GO - CC	2.29	0.03	2.26	2.15×10−12
Response to wounding	GO - BP	3.35	0.03	1.69	0.09
Cell adhesion	GO - BP	3.23	0.06	1.87	0.0008
Cytokine-cytokine receptor interaction	KEGG	12.30	6.3 × 10−6	2.17	0.01
Hematopoietic cell lineage	KEGG	17.09	0.001	3.07	0.04
ECM-receptor interaction	KEGG	34.18	0.001	2.90	0.08

The fold enrichment is calculated by DAVID as the proportion of genes that are part of a given pathway among those associated with ulceration divided by the equivalent proportion in the background list. Abbreviations used: GO-BP: Gene Ontology Biological Process; GO-CC: Gene Ontology Cellular Component; KEGG: Kyoto Encyclopedia of Genes and Genomes, BH FDR: Benjamini-Hochberg false discovery rate.