Multipotent Adult Progenitor Cells (MAPC) are bone marrow derived cells with extended differentiation potential. With their capability to expand ex vivo without senescence, MAPC possess great potential for cell therapies, tissue engineering and is an ideal model for in vitro differentiation of stem cells to specific lineages. Clonally isolated MAPC show different expression levels of the transcription factor oct-4, a marker of mouse and human embryonic stem cells (ESC) involved in maintaining pluripotency. These cells also exhibit variable level of differentiation potential towards endodermal and mesodermal lineages that correlates with oct-4 expression. Oct-4 is downregulated as mouse and human embryonic stem cells differentiate. The biological significance of oct-4 expression in adult stem cells has not been elucidated neither its use as a marker of cells with extended differentiation potential in adult stem cells been explored. The lack of markers that correlate with differentiation potential of adult stem cells has hindered the cell culture process development and optimization needed for wide spread application of these cells. Gene expression profiles of mouse MAPC clones expressing different levels of oct-4 (0, 0.1, 5 and 10% of that in ES cells) were compared to lineage restricted Mesenchymal Stem Cells (MSC) and pluripotent ESC by using Affymetrix microarrays. Approximately 20,000 of over 45,000 probes present on the array were differentially expressed with an FDR of 0.2%. Principal component analysis yielded three principal components that capture 93% of the total variability among groups. These principal components allowed for separation of the groups that correlate with oct-4 expression. While oct-4 expressing MAPC are clustered all together, they are well separated from the non-oct-4 expressing MAPC. Furthermore MAPC expressing oct-4 are significantly closer to ESC whereas non-oct-4 expressing MAPC are closer to MSC. The contributing genes to a given component bear biological significance as they are associated with the differentiation potential or lineage commitment of each of the cell populations. Visualization of genes in this three dimensional space reveals that oct-4 positive MAPC express early endodermal and mesodermal transcription factors including GATA-4, GATA-6, Sox7, and Sox17. PCA also clearly shows a negative association of transcription factors required for maintenance of ESC pluripotency and expression of lineage related transcription factors. The analysis was also applied for membrane components to identify candidate markers of stem cells from adult bone marrow. Principal component analysis on the transcriptomes of different stem cell populations thus successfully grouped them according to their differentiation capacity and provides insights on the genes that control pluripotency and lineage commitment.