L functions only a rather small number of imprinted genes (7 genes) show a functional association to the nervous system [22]. Several publications have pointed out that imprinted genes play roles in placenta morphology and function. We do not observe a specific association with GO terms that are specifically related to the placenta. Hence, at the first glance our results do not supportFigure 5. The enriched GO terms of biological functions for the paternally Title Loaded From File expressed genes in human. Nodes represent the enriched Go terms and the thickness of the interconnected links corresponds to the number of shared genes. doi:10.1371/journal.pone.0050285.gCellular Functions of Genetically Imprinted GenesFigure 6. Conserved transcription factors in the full set of imprinted genes in human (a) and mouse (b) at p-value of 0.01. Marked in red and blue in the top line are the maternally, paternally expressed genes, respectively. Genes that are imprinted in both species are marked in green. Pink are the genes shown to be imprinted only in human, and brown are the genes shown to be imprinted only in mouse. doi:10.1371/journal.pone.0050285.gCellular Functions of Genetically Imprinted Genesspecific roles in the placenta. However, one should note that many genes that show an expression bias towards the maternal allele in the placenta but not in the embryo have been excluded from this analysis. This was done since it is still under discussion if such biases might be mostly caused by sample contamination with maternal tissue [23]. When paternally and maternally expressed genes are analyzed separately, mouse and human show clearly different associations. In the human, several maternally expressed genes (DLX5, GNAS, TP73, PHLDA2, CDKN1C, PPP1R9A, UBE3A) are associated with organ morphogenesis, and more particularly with nervous system development and oesteoblast differentiation. In the mouse, maternally expressed genes form two functional networks that are clearly separated. One is related to transport processes, and includes carrier proteins and channel proteins. Especially transport processes that are a key feature of placenta function are specifically associated with maternally expressed genes in the mouse. The second network consists of terms related to G protein signaling. This network is clearly dominated by CALCR and SLC22A18. For the paternally expressed genes, a functional network is only found in the human. This 1516647 network consists mostly of terms associated with development, and a few terms that are related to gene regulation. Interestingly, several imprinted genes that encode transcription factors (PLAGL1, L3MBTL, WT1, ZIM2, PEG3) seem to be key players in this network. Nevertheless, also among the maternally expressed genes are genes that regulate transcription. Thus, regulatory functions are not an exclusive feature of paternally expressed genes. The differences between mouse and human can in parts be explained by evolutionary divergence. For example, human and mouse placentae show pronounced differences in morphology. In a previous publication we have shown that especially maternally expressed genes experienced an accelerated sequence divergence that were less prominent in the human [6]. These differences in molecular Title Loaded From File evolution might be associated with functional differences. In this context we will briefly consider possible biases in the results obtained. The annotations stored in the Gene Ontology of course only represent a fraction of all knowledge.L functions only a rather small number of imprinted genes (7 genes) show a functional association to the nervous system [22]. Several publications have pointed out that imprinted genes play roles in placenta morphology and function. We do not observe a specific association with GO terms that are specifically related to the placenta. Hence, at the first glance our results do not supportFigure 5. The enriched GO terms of biological functions for the paternally expressed genes in human. Nodes represent the enriched Go terms and the thickness of the interconnected links corresponds to the number of shared genes. doi:10.1371/journal.pone.0050285.gCellular Functions of Genetically Imprinted GenesFigure 6. Conserved transcription factors in the full set of imprinted genes in human (a) and mouse (b) at p-value of 0.01. Marked in red and blue in the top line are the maternally, paternally expressed genes, respectively. Genes that are imprinted in both species are marked in green. Pink are the genes shown to be imprinted only in human, and brown are the genes shown to be imprinted only in mouse. doi:10.1371/journal.pone.0050285.gCellular Functions of Genetically Imprinted Genesspecific roles in the placenta. However, one should note that many genes that show an expression bias towards the maternal allele in the placenta but not in the embryo have been excluded from this analysis. This was done since it is still under discussion if such biases might be mostly caused by sample contamination with maternal tissue [23]. When paternally and maternally expressed genes are analyzed separately, mouse and human show clearly different associations. In the human, several maternally expressed genes (DLX5, GNAS, TP73, PHLDA2, CDKN1C, PPP1R9A, UBE3A) are associated with organ morphogenesis, and more particularly with nervous system development and oesteoblast differentiation. In the mouse, maternally expressed genes form two functional networks that are clearly separated. One is related to transport processes, and includes carrier proteins and channel proteins. Especially transport processes that are a key feature of placenta function are specifically associated with maternally expressed genes in the mouse. The second network consists of terms related to G protein signaling. This network is clearly dominated by CALCR and SLC22A18. For the paternally expressed genes, a functional network is only found in the human. This 1516647 network consists mostly of terms associated with development, and a few terms that are related to gene regulation. Interestingly, several imprinted genes that encode transcription factors (PLAGL1, L3MBTL, WT1, ZIM2, PEG3) seem to be key players in this network. Nevertheless, also among the maternally expressed genes are genes that regulate transcription. Thus, regulatory functions are not an exclusive feature of paternally expressed genes. The differences between mouse and human can in parts be explained by evolutionary divergence. For example, human and mouse placentae show pronounced differences in morphology. In a previous publication we have shown that especially maternally expressed genes experienced an accelerated sequence divergence that were less prominent in the human [6]. These differences in molecular evolution might be associated with functional differences. In this context we will briefly consider possible biases in the results obtained. The annotations stored in the Gene Ontology of course only represent a fraction of all knowledge.
