Is of particular interest to analyze which of these functions are

Is of particular interest to analyze which of these functions are controlled by the sets of maternally and paternally KDM5A-IN-1 expressed genes, we have also separately analyzed the enrichment of GO terms in these two groups.map enrichment plugin in Cytoscape [11] was used to visualize the overrepresented order 58-49-1 functional terms and display the overlapping functional sets.Gene Functional clusteringClustering and grouping of the imprinted genes were performed using the DAVID gene functional classification tool. This tool employs a set of fuzzy clustering techniques to classify input genes into functionally related gene groups (or classes). This is done on the basis of the co-occurrence of annotation terms by generating a gene-to-gene similarity matrix based on shared functional annotation. This switches the functional annotation 25033180 analysis from a gene-centric analysis to a biological module-centric analysis [10]. The similarity threshold was set to the minimum similarity threshold of 0.3 suggested by the DAVID consortium. This is then the minimum value to be considered by the similarity-matching algorithm as biologically significant. Also, we set the minimum gene number in a seeding group to 2. This would be the minimum size of each cluster in the final results. All remaining parameters were kept to their default values. The results of the functional classification tool are visualized as heat maps to show the corresponding gene-annotation association across the clustered genes.Methods Gene SelectionImprinted genes of human and mouse were downloaded from the Catalogue of Imprinted Genes and Parent-of-origin Effects in Humans and Animals (IGC) [9] and [2]. The catalogue encompasses genes that were described as being imprinted in literature. As the related experiments were done in many different labs, the experimental procedures differed considerably. After reading the original publications, we manually selected 64 imprinted genes that are imprinted without doubt in at least one of the two species, see table S1. For the gene C15orf2, the expressed allele is unknown since there is no information on the parental origin of the alleles. Copg2, and Zim2 are paternally expressed in the human, but maternally expressed in the mouse. Grb10 exhibits isoform-specific imprinting effects, i.e. there are paternally expressed and maternally expressed isoforms. The other 60 genes have been experimentally classified into paternally and maternally expressed alleles in two equal halves. 25 genes are imprinted in both species, for the 1326631 remaining imprinted expression was proven only for one of the two species. As control group for the human (mouse) imprinted genes we used all human (mouse) genes that are annotated in the Gene Ontology.Transcription Factor Target EnrichmentThe web-based gene set analysis toolkit WebGestalt [12] was used to analyze the targets of transcription factors (TFs), see tables S7 and S8. This tool incorporates information from different public resources such as NCBI Gene, GO, KEGG and MsigDB (http://bioinfo.vanderbilt.edu/webgestalt/). Using the TF target analysis tool implemented in WebGestalt, we analyzed whether a set of genes is significantly enriched with TF targets (TFT). TFT’s are specific sets of genes that share a common TF-binding site defined in the TRANSFAC database [13]. TFT’s are collected in the Molecular signature Database (MsigDB) [14] and are retrieved by WebGestalt upon analysis request. The examined promoter region has the size of 22 kb.Is of particular interest to analyze which of these functions are controlled by the sets of maternally and paternally expressed genes, we have also separately analyzed the enrichment of GO terms in these two groups.map enrichment plugin in Cytoscape [11] was used to visualize the overrepresented functional terms and display the overlapping functional sets.Gene Functional clusteringClustering and grouping of the imprinted genes were performed using the DAVID gene functional classification tool. This tool employs a set of fuzzy clustering techniques to classify input genes into functionally related gene groups (or classes). This is done on the basis of the co-occurrence of annotation terms by generating a gene-to-gene similarity matrix based on shared functional annotation. This switches the functional annotation 25033180 analysis from a gene-centric analysis to a biological module-centric analysis [10]. The similarity threshold was set to the minimum similarity threshold of 0.3 suggested by the DAVID consortium. This is then the minimum value to be considered by the similarity-matching algorithm as biologically significant. Also, we set the minimum gene number in a seeding group to 2. This would be the minimum size of each cluster in the final results. All remaining parameters were kept to their default values. The results of the functional classification tool are visualized as heat maps to show the corresponding gene-annotation association across the clustered genes.Methods Gene SelectionImprinted genes of human and mouse were downloaded from the Catalogue of Imprinted Genes and Parent-of-origin Effects in Humans and Animals (IGC) [9] and [2]. The catalogue encompasses genes that were described as being imprinted in literature. As the related experiments were done in many different labs, the experimental procedures differed considerably. After reading the original publications, we manually selected 64 imprinted genes that are imprinted without doubt in at least one of the two species, see table S1. For the gene C15orf2, the expressed allele is unknown since there is no information on the parental origin of the alleles. Copg2, and Zim2 are paternally expressed in the human, but maternally expressed in the mouse. Grb10 exhibits isoform-specific imprinting effects, i.e. there are paternally expressed and maternally expressed isoforms. The other 60 genes have been experimentally classified into paternally and maternally expressed alleles in two equal halves. 25 genes are imprinted in both species, for the 1326631 remaining imprinted expression was proven only for one of the two species. As control group for the human (mouse) imprinted genes we used all human (mouse) genes that are annotated in the Gene Ontology.Transcription Factor Target EnrichmentThe web-based gene set analysis toolkit WebGestalt [12] was used to analyze the targets of transcription factors (TFs), see tables S7 and S8. This tool incorporates information from different public resources such as NCBI Gene, GO, KEGG and MsigDB (http://bioinfo.vanderbilt.edu/webgestalt/). Using the TF target analysis tool implemented in WebGestalt, we analyzed whether a set of genes is significantly enriched with TF targets (TFT). TFT’s are specific sets of genes that share a common TF-binding site defined in the TRANSFAC database [13]. TFT’s are collected in the Molecular signature Database (MsigDB) [14] and are retrieved by WebGestalt upon analysis request. The examined promoter region has the size of 22 kb.

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