Fig. 2
Genes regulated by LIF at 1 h. Cells cultured for 1 day in GM were switched to DM; after 3 h EPO with or without LIF was added and cells were incubated for further 1 h. a Flow chart. Genes regulated by differentiation were selected by comparing differentiating (4 h culture with DM) vs undifferentiated cells; genes regulated by EPO by comparing EPO-treated (1 h) vs untreated differentiating cells; genes regulated by LIF by comparing EPO + LIF-treated (1 h) vs EPO-treated cells. Cut-off for selection was FC of 1.5 (log2 FC of 0.58) and BH adj. P value < 0.05. The number of upregulated or downregulated genes resulting from filtering is indicated. Negative regulators induced by LIF and unchanged by differentiation or EPO (47) or decreased by differentiation (28) are highlighted in red. b Gene-gene interaction network of the putative negative regulators increased by LIF at 1 h. All the genes increased by LIF and either unchanged by differentiation or EPO (47 genes, Fig. 2a) or decreased by differentiation alone (28 genes, Fig. 2a) were analysed with the STRING software and the gene-gene interaction network was visualised. None of the genes increased by LIF were decreased by EPO at this time point. Different line colours represent types of evidence for association: green line, neighbourhood evidence; red line, fusion evidence; purple line, experimental evidence; light blue line, database evidence; black line, co-expression evidence; blue line, co-occurrence evidence; yellow line, text mining evidence. The full list of all the 75 genes and the relative expression changes induced by LIF and by differentiation are reported in Additional file 3