Spinel (magnesium aluminate MgAl2 O4 ) ceramic-based polyphasic composite scaffold has been recently reported for craniofacial bone tissue engineering. Improving the osteogenic effects of such composite scaffolds with bone morphogenetic proteins (BMP2) is an intensely researched area. This study investigated the gene interactions of this scaffold with BMP2 and mesenchymal stem cells (MSCs). Human bone marrow MSCs were cultured in 3 groups: Group 1-Control (BMSCs), Group 2-BMSC with BMP2, and Group 3-BMSC with scaffold and BMP2. After RNA isolation, gene expression analysis was done by microarray. Differentially expressed genes (DEGs) (-1.0 > fold changes>1 and p value <.05) were studied for their function and gene ontologies using Database for Annotation, Visualization and Integrated Discovery (DAVID). They were further studied by protein-protein interaction network analysis using STRING and MCODE Cytoscape plugin database. Group 3 showed up regulation of 3222 genes against 2158 of Group 2. Group 3 had five annotation clusters with enrichment scores from 2.08 to 3.93. Group 2 had only one cluster. Group 3 showed activation of all major osteogenic pathways: TGF, BMP2, WNT, SMAD, and Notch gene signaling with effects of calcium and magnesium released from the scaffold. Downstream effect of all these caused significant activation of RUNX2, the key transcriptional regulator of osteogenesis in Group 3. STRING and MCODE Cytoscape plugin demonstrated the interactions. The enhanced MSC differentiation for osteogenesis with the addition of BMP2 to the polyphasic composite scaffold proposed promising clinical applications for bone tissue engineering.