![]() MiRNAs are important gene regulators, therefore it is essential include them in the interactome. Alternatively, if using the human interactome from the BioGRID website the gene names are used automatically, rather than Entrez ID. Once completed, all nodes in the interactome should now show their gene name ( Fig. Download the gene names from DAVID and import into Cytoscape using file > import. Import the ‘Entrez ID’ list into DAVID to identify the gene names and abbreviations for each node. ![]() Export the merged interactome node list from Cytoscape and remove all columns except the ‘Entrez ID’. This was conducted using the online tool DAVID ID ( ). To select nodes from the miRNA target lists, which are downloaded as gene names, all nodes need to be changed to their respective gene name. C) Screenshot of the DAVID output of the conversion from Entrez ID to Gene Name. B) Screenshot of the UCSC Genome Browser highlighting the location of the transcription factors of the selected gene or miRNA. Transcription factor list of hsa-miR-496 as extracted from the UCSC Genome Browser (Right Panel). A) Gene target list for hsa-miR-33a (Left Panel). txt files created for the miRNAs of interest. It was this smaller interactome that was used for further network filtering and annotation, after the removal of duplicated edges and self-loops. This interactome contains the genes that directly interact with the viral oncoproteins, and their relationship with other human genes. This produces a smaller secondary network, as shown in Fig. To tidy up this new network, select Edit > Remove Duplicated edges, and Edit > Remove Self-Loops. Once all nodes of interest are selected, a new network is created by selecting File > New > Network > from Selected nodes, Selected edges. This was done by searching for these two HPV16 oncogenes within the network, and selecting their first neighbors. This ensures for easier identification of the two genes in subsequent network creation.įor our example on HPV16, the two major oncoproteins E6 and E7 were selected, along with their direct interactors (first neighbors). The HPV16 viral oncoproteins, E6 and E7, were searched for using the search network tool, and their respective nodes were moved away from the main interactome. This approach can be broadly applied to understand and map the regulatory functions of other oncogenic viruses, and determine their role in altering the cellular environment in cancer.Īvailability and Implementation Cytoscape (Shannon et al. To demonstrate this, we constructed a gene regulatory interactome encompassing Human Papillomavirus Type 16 (HPV16) and its control of specific miRNAs. This method may be applied to identify specific pathways that are altered in viral infection, and contribute to the oncogenic transformation of cells. We detail a logical step-by-step guide to uncover viral-protein-miRNA interactions using publically available datasets and the network building program, Cytoscape. A thorough understanding of the molecular pathways and individual genes altered by oncogenic viruses is needed for the identification of targets that can be utilised for early diagnosis, prevention, and treatment methods. It is currently difficult to determine the effect of oncogenic viruses on the global function and regulation of pathways within mammalian cells.
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |