To extend its functionality also get CluePedia. ClueGO is easy updatable with the newest files from Gene Ontology, KEGG and Reactome. It will operate on any generic enrichment results as well as specifically on Gene Set Enrichment Analysis (GSEA) results and uses GO to identify functional enrichment categories.ĬlueGO: Creates and visualizes a functionally grouped network of terms/pathways. BinGO also allows you to interactively select components of a network analysis and test this subset for enriched GO terms.Įnrichment Map: This app allows you to visualize the results of gene-set enrichment as a network. The complete list of Cytoscpae apps is found here, and apps are listed by analysis categories.įor example, apps that do enrichment analysis include:īinGO: a biological network Gene Ontology tool that determines which GO categories are statistically over-represented in a set of genes. Once you have Cytoscape installed, you may also add specific apps. More about Cytoscape is here and you can download cytoscape for your use here. Its ability to different analyses basedupon different apps, makes Cytoscape a flexible functional modeling tool that requires only a small start up requirement. There are many plugins or apps available for bioinformatics analysis, including pathways analysis and generating networks. This may be what you expect from an analysis where you have mapped cassava to Arabidopsis pathways.ĥ.2 Task 2: Using Cytoscape and Cytoscape AppsĬytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. Note that there are Photosynthesis pathways at top, followed by conserved metabolic pathways. You can click on column headings to sort these columns. The displayed Table shows pathways (along with their pathway IDs and database), sample and background numbers and Pvalues. You can check the details of the job in the 'Analysis history' page. The job has been finished, and the result is shown here in this window. Output: change the output file to cassava.identify to make it easier to find. Options for statistics - advanced options (use default) Leave this option blank (to use the default background set) Leave these as the default settings.įor Background (defined by user or default)Īnnotate result of another gene set (If no annotate file provided, KOBAS will use genes from whole genome as default background): This shows KEGG Pathway, BioCyc and Reactome databases checked. The table below will show the input IDs and the Arabidopsis accessions they were mapped to.Ĭlose file and click on IDENTIFY on left hand side toolbar.įor Sample file (result of Annotate): use dropdown menu to select cassava.annotateĬlick on "Show available databases according to the species used in sample input Species and Databases". This means that 6 of the sequences were unable to be mapped to Arabidopisis. You will see the message: 94 succeed, 6 fail When status shows as finished, click on output file link You can check the latest status of job in "history" menu. Output file: Change the output file name to "cassava.annotate" so that you can more easily find it.Įmail (you will be informed by email when your long job is finished): for longer examples, you may want to supply your email. Save result in directory: use the default work directory. Note that for your own data set you should a species that is closely related to your species of interest. In the Input section of KOBAS make sure "Use which file source?" has Paste from clipboard selected and paste the fasta formatted cassava sequences into the text box.įor File type: select "fasta protein sequence" from the dropdown menu.įor "To which species do you want to map these genes? (If you want to map the genes to KO terms, please select 'KO')" use the drop down menu to select A. We will use the cassava protein list from tutorial 3. Start by selecting "Annotate" from the left hand side toolbar. KOBAS 2.0 works off KEGG data to map pathways based upon orthology or similarity and then search for enrichment of these pathways. 5.2.2 Using BinGO to do enrichment analysis.5.2.1 Installing and starting the BinGO app in Cytoscape.5.2 Task 2: Using Cytoscape and Cytoscape Apps.We will use KOBAS to look for pathways enrichment and demonstrate the use of Cytoscape and its apps functional modeling. In this tutorial we will use non-commercial pathways and enrichment analysis tools. Tutorial 5: Pathways and networks enrichment analysis tools COST Functional Annotation of Genome Sequences in Agriculural species Workshop
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