Regassa et al. BMC Genomics 2011, 12:57 http://www.biomedcentral.com/1471-2164/12/57 Page 10 of 20 Figure 10 An example of a gene network, showing the relationships between molecules identified by the microarray and over expressed in oocytes cultured with their companion CCs. The type of the association between two molecules is shown as a letter on the line that connects them. The number in parenthesis next to the letter represents the number of bibliographic references currently available in the Ingenuity Pathways Knowledge Base that support each one of the relationships. Direct or indirect relationships between molecules are indicated by solid or dashed lines connecting them, respectively. P = phosphorylation, A = gene activation,E = increase in expression, PP = protein-protein interaction, PD = protein-DNA binding, MB = membership in complex, LO = localization, L = proteolysis, RB = regulation of binding. transcriptome profile changes when either cell type matures with or without the other using Affymetrix GeneChip Bovine Genome Array. Here, we identified for the first time, transcripts that are exclusively expressed in bovine oocytes or CCs at GV and MII stages. Identifying specific transcription programs either in oocyte or CCs has a paramount importance in RNAi based gene function study. Knowledge of genes exclu- sively expressed either in oocyte or CCs would enable researchers to select the appropriate design for func- tional analysis of genes and route of introducing RNAi agents into COC. For instance, if a given gene is expressed only in CCs, transfection is the best method of introducing anti-sense oligomers into the complex. Identification of such genes would help also in under- standing functional biological processes and pathways specific to either oocyte or CCs. Additionally, we assessed the effect of removing the bi-directional communication axis on the gene expres- sion profile of either cell during in vitro maturation and transcriptome profile changes associated with the transition of CCs from GV to MII stage at global scale. Identification of genes that are significantly affected when either the oocyte or CCs mature with or without one or the other would be vital to understand the most important cellular and molecular functions that are associated with the acquisition of developmental competence. Figure 11 An example of a gene network, showing the relationships between molecules identified by the microarray and over expressed in CCs cultured with the enclosed oocytes relative to those cultured without. The type of the association between two molecules is shown as a letter on the line that connects them. The number in parenthesis next to the letter represents the number of bibliographic references currently available in the Ingenuity Pathways Knowledge Base that support each one of the relationships. Direct or indirect relationships between molecules are indicated by solid or dashed connecting lines, respectively. P = phosphorylation, A = gene activation, E = increase in expression, PP = protein-protein interaction, PD = protein-DNA binding, MB = membership in complex, LO = localization, L = proteolysis, RB = regulation of binding. Specific expression program is exhibited by bovine oocyte and CCs In addition to the previously identified ones [42,59], this study identified several oocyte or CCs specific transcripts that may play important biological roles in the bi-directional communication of the two cell types during in vitro maturation and for the acquisition of developmental competence at latter stages. Hierarchi- cal clustering of differentially expressed genes demon- strated that the expression profile of oocyte is markedly different from that of its companion CCs with the latter having more number of transcripts than the former. Transcripts that are over expressed in oocytes are involved in processes leading to meiotic maturation. We found considerably higher (more than 1024 fold change) and exclusive expression of GDF9, BMP15, MOS, Zona Ppellucida Proteins (ZP2, 3, 4), NLRP5, RBM35A, TACSTD1, GAS7 and others in oocyte compared with CCs. Since the roles of GDF9 and BMP15 in oocyte