Regassa et al. BMC Genomics 2011, 12:57 http://www.biomedcentral.com/1471-2164/12/57 Page 7 of 20 Figure 3 Hierarchical clustering and heat map of some of the top genes over expressed in GV oocytes (A) and CCs (B) with a fold change of more than 1024. Abbreviations, GVOO and GVCCs stand for germinal vesicle oocyte and cumulus cells, respectively. Numbers (1, 2, and 3) indicate the three biological replicates used for microarray hybridization. post transcriptional modification are also observed. Simi- larly, 90 of the genes over expressed in CCs + OO, repre- senting 34% of the total are classified under cellular growth and proliferation. A graphical representation of this functional classification of the genes over expressed in OO + CCs and CCs + OO are shown in Figures 8 and 9, in which 16 and 12 functional groups with higher P-values are noted. Some of these groups shared several common genes. In addition, 28 and 23 of the genes over expressed in OO + CCs and CCs + OO relative to OO - CCs and CCs - OO respectively, are assigned to 5 and 8 different canonical pathways (Additional files 14 and 15). Finally, these genes from the two groups were mapped on 5 top networks each network containing genes from the input data that shared known direct or indirect relationships. Examples of networks created from our data are shown in Figures 10 and 11, where the relationships between mole- cules that were over expressed in OO + CCs and CCs + OO are represented by the arrows that connect them. Fig- ure 10 shows a complex network that plays an important role in gene expression, small molecule biochemistry and Figure 4 Hierarchical clustering and heat map of some of the top over expressed genes in MII oocytes (A) and CCs (B) with a fold change of more than 512. Abbreviations, MIIOO and MIICCs stand for metaphase II oocyte and cumulus cells, respectively. Numbers (1, 2, and 3) indicate the three biological replicates used for microarray hybridization.