Stimulus-dependent differences in signalling regulate epithelial-mesenchymal plasticity and change the effects of drugs in breast cancer cell lines

Table 1 Different signalling pathways are dysregulated between the models of in vitro induced EMT

*differential analysis between:*	Cell Lines	PMC42-ET	PMC42-LA	MDA-MB-468	MDA-MB-468	PMC42-ET vs. PMC42-LA	PMC42-ET vs. PMC42-LA	MDA-MB-468
*differential analysis between:*	Conditions	+EGF vs. Unstim.	+EGF vs. Unstim.	+EGF vs. Unstim.	+HPX vs. Unstim.	Unstim.	+EGF	+HPX vs +EGF
	number of differentially expressed transcripts	238	591	3155	3716	3261	2938	1626
KEGG signalling pathway/system:	PI3K-Akt	0.015	0.000	0.030	0.005	0.153	0.559	0.943
	HIF-1	0.952	0.244	0.002	0.002	0.982	0.732	0.000
	Rap1	0.562	0.014	0.000	0.000	0.175	0.075	0.742
	Hippo	0.173	0.000	0.022	0.085	0.004	0.297	0.996
	Wnt	0.015	0.371	0.038	0.071	0.002	0.455	0.534
	MAPK	0.214	0.044	0.312	0.680	0.360	0.634	0.768
	Hedgehog	0.977	0.000	0.999	0.939	0.217	0.093	0.993
	TGF-beta	0.029	0.000	0.215	0.328	0.053	0.632	0.694
	Ras	1.000	0.169	0.259	0.022	0.120	0.065	0.783
	Phosphatidyl-inositol	0.796	0.833	0.238	0.049	0.753	0.923	0.893
	cAMP	0.992	0.639	0.242	0.017	0.983	0.756	0.201

The first row shows the number of mRNA transcripts with a significant (q-value < 0.05) difference in abundance between the specified cell lines or conditions. Subsequent rows show the estimated p-value for enrichment of elements within KEGG pathways without correction for multiple hypothesis testing. KEGG maps related to signal transduction with a significant (p-value < 0.05) enrichment in at least one comparison are shown (for a complete list please refer to Additional file 8: Table S2). Values in bold are statistically-significant following a Bonferroni correction for multiple hypothesis testing (adjusted p-value < 0.05; n = 22 ‘signalling pathway’ KEGG maps), p-value entries greater than 0.10 are in grey.

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