There are 3 possible behaviours, and you can change them by clicking on the appropiate one: If you have nodes on the visualization, you can determine what the application will do when you click on them. This is useful when wanting to work with a more accurate network, or when the nodes displayed on the visualization is too high. Interactions by the desired cut-off, and then removing all the unconnected nodes. You can use this function in conjuction with the Remove Unconnected button to filter the graphs first filtering the Note that the hidden interactions are not removed, so you can get them back by using another cut-off. With this slider you can hide the interactions using the percentage of votes of the random forest classifier as a cut-off. Use together with Filter interactions to filter networks. Note that this applies to all types of connection (homology or interactions). It will NOT add any node.Īctivating this button will remove all the nodes without a visible connection. This button will add all the interactions between the nodes displayed on the visualization. Turning this option On or Off will not change the layout of the planarian nodes. They behave as all the other nodes, but with the exception that you can't Expand them. When changing this switch to On, the homologs of the displayed planarian contigs will be drawn on the visualization. Take note that some layouts will change each time you run them. When you select it, the layout will be run on the display,Īnd the positions of the nodes will change. Using this dropdown menu you can select the layout of the network. Note that you will not lose the network already displayed on the left, so you can add nodes individually without losing the visualization.Īll the nodes for which you have searched (either using this search function or by "expanding" them, see below) will be outlined in green, Once you have typed the symbols you want to look for, and have selected the appropiate dataset, click on the button + Add. You can use 4 types of symbols to do that: In order to search for contigs, you have to select a Dataset (a planarian transcriptome for which we predicted an interactome), and then look for contigs. These nodes will be connected by edges (lines),Īnd each type of them will have a different meaning: Will represent a contig (for planarian datasets) or a protein (for the Human reference dataset). Use the menus on the right to manipulate the graph, which will display on the left side of the screen. NetExplorer allows users to explore the predicted networks dinamically, adding and removing nodes from several interactomes. If you want to see the card in full-screen mode in a new tab (for example, to print it), click on. You can also navigate back using your browser's back button ←.Ĭlose the card using your Esc key or the x button on the top right. You can navigate through different contigs/proteins without losing the results from GeneSearch, NetExplorer or PathwayFinder: only the information card will change. Here, you will be able to download FASTA sequences, look for the annotated homolog for each contig, look for annotated PFAM domains, GO codes, and predicted interactions. If the selected dataset was a Planarian transcriptome, the Human homolog will be specified inside the box, as can be seen in the image.Ĭlick on any of the boxes to get an information card, which will contain a summary of the information stored for that particular protein or contig.Īn information card is a brief summary of a contig or protein stored in any of our interactomes. The symbol on the top right of each box always represents the database to which the symbol belongs. If there are proteins/contigs in the selected dataset that satisfy the search criteria, you will get a list of symbols inside blue boxes (see image). You can mix the different types of symbols in the same search, e.g. You can do multiple searches at once, using commas ',' to separate each item. This will retrieve all the planarian contigs with the specified PFAM annotated through our protocol (that is, with HMMER with a e-value cutoff of 10 -10). This will display all the planarian contigs with a human homolog with the specified GO code. THOC* will display the nodes homologous to THOC, THOC1, THOC2, THOC3, THOC4, THOCXX, etc. This will retrieve all the homologous contigs to the specified human protein. cth1_Trc_comp11081_c0_seq1 (for dataset Cthulhu) Contig identifiers (which will be specific to each transcriptome).Then, write one of the following types of symbols: In order to search contigs/proteins, you have to select one of the available datasets (planarian or Human). GeneSearch allows users to look for proteins/contigs across the different planarian transcriptomes and Human reference interactome.
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