Using microarray technology it has been possible to identify genes both induced by LIF and differentially expressed upon Oct4 knockout in the ZHBTc4.1 cell system. Analysis of the biological function of two genes from the LIF pathway (Egr1 and Gbx2) revealed altered morphology, transcriptome and putative ability to self-renew upon over-expression. The analysis of genes enriched in ES cells compared with trophoblast and neural stem cells, which are subsequently down-regulated upon Oct4 deletion revealed 42 genes including; Nr0b1 and 8430410A17Rik. Enrichment analysis combined with examination of the convergence between the LIF/Stat3 and Oct4 pathways revealed Klf2, Klf4 and Klf5 as genes which are tightly associated with pluripotency. Klf2 has the ability to engage long term LIF-independent self-renewal in Lifr^-/- ES cells. Long term culture of mES cells is associated with karyotypic changes which seemingly enhance self-renewal at the expense of pluripotent contribution. Understanding selection may identify genes and loci with novel functions in self-renewal. Using array based comparative genome hybridisation (aCGH) it was possible to identify a recurrently aberrant region on chromosome 14, which contains Rb1, Spry2 and Klf5. Trisomy chr. 11, amplification of a 37Mb region containing the Nanog locus on chromosome 6 and an 11Mb deletion on chromosome 17 were also discerned. The regions on chromosomes 6 and 11 are syntenic with recurrently aberrant regions in human ES cells, implying conservation of either the mechanism of aberration, or a selective pressure that is retained across different species of ES cell. Utilisation of array-based technologies has facilitated the identification of number genes which are enriched in mES cells and are rapidly down-regulated upon Oct4 deletion, some of which are also implicated in the LIF/Stat3 pathway. One gene in particular; Klf2 a member of the Krüppel-like family is capable of maintaining cytokine independent self-renewal upon over-expression. Klf4 and Klf5 also seem to be entwined with Oct4 and LIF/Stat3 function. Karyotypic aberrations in mES cells were also identified, which represent putative selective loci which may shift the balance between self-renewal and survival over differentiation and death.