← Revision 3 as of 2008-08-14 12:21:51
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''__Plugins to Load__'': MimiPlugin | ''__Plugins to Load__'': MiMiPlugin |
MiMiPpiDiscoveryRecipe
Barbara Mirel, Piet Molenaar
Your institute
Biological Use Case: Describe a real biological problem.
Recipe
Cytoscape version: 2.6
Plugins to Load: MiMiPlugin
GUI steps:
Describe each step (story), the GUI action to take, and probable remarks
Story |
Action |
Remarks |
1. Today we will demonstrate how to interact with the MiMI database. This mechanism is a Discovery approach starting from a single protein of interest to explore other possible protein interactions |
Bring up Cytoscape window, pre-loaded with TCF7L2 |
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1.a.i. We will show how to use the Mimi Plug-in for Cytoscape to retrieve protein interactions, and to visually display them. We will highlight certain features of the Mimi Plug-in. Firstly input search parameters |
Search parameters for single gene and file |
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1.a.ii. Secondly show the text panel for nodes |
CTRL A to select all nodes. Open the text panel and select: Description, Gene, Other Gene Names, process, function, and Pathways |
Show that columns can be switched and be sorted on |
1.b.i. We will show the seamless integration between Cytoscape and the SAGA tool. SAGA is a subgraph approximate matching tool written by Yuanyuan Tian in the laboratory of Dr. Jignesh Patel. |
Select ALL nodes (CTRL+ALT+A) Right Click and select SAGA. Show the scoring and matches between the submitted network and the KEGG Matching pathways |
Blue lines are matching relationships, Red Lines are matching proteins |
1.b.ii. Show how this links to the annotated KEGG Pathway |
by clicking on the “Link to KEGG Picture” at the top of the match. Show how the matches to your submitted proteins align to this picture. |
Tian Y, McEachin RC, Santos C, States DJ, Patel JM. SAGA: a subgraph matching tool for biological graphs. Bioinformatics. 2007; 23(2):232-9. |
1.c. Edge information description |
All nodes and edges should still be selected when you return to Cytoscape window. Click on the Edge Attribute tab at bottom and choose attributes: Genename, Provenance and Type. Show how to sort, and how to identify in the image which edge you’ve selected |
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1.d. We will show how the Mimi provenance is visible through the browser |
Discuss MIMI Provenance here, and show NLP Only attributed relationships. |
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1.e. We will show you the integration of the parsed PubMed abstract literature data (bioNLP) , and how to connect out to pubmed for the abstract information if needed. |
Returning to a single edge, we select PARP1 and TCF7L2 edge and right click to get BioNLP data. Discuss 3 different Abstracts and ability to link out. Mention MEAD summarization for large numbers of sentences – don’t demo this |
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Data / Session Files: Attach (preferably) a session file or else the data files used in the workflow
Presentation: Attach your presentation
Webstart: Attach a webstart
Video: Attach a video link