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01_​Protein_​Interaction_​Network_​Solution

PPI Network New

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Activity II: Network Creation and Visualization1. Start by executing the provided Visualization Property Extractor node.2. On the configuration dialog of the provided Object Inserter node, set Node id column = protein1, Second node id column = protein2 and Edge id column = <RowID>.On the advanced options tab set Node partition column = protein1.3. Similarly, configure the Feature Inserter node with: Node id column = protein2, Name=Color, Value column = color and Type = based on value column4. Connect a Network Viewer node to the Feature Inserter node and configure it as follows: Layout Settings => Layout = cose and Node Settings => Fill color = color5. Connect the output of the Table Editor node to the second input port of the Network Viewer node.6. Connect an Excel Writer (XLS) node to the output of the provided Row Filter node and configure it by providing a file location.7. Create a component containing the nodes starting from Cleanup metanode to the Network Viewer and Row Filter nodes (excluding the Excel Writer (XLS) node). (Hint: To create a component, select the nodes to be included in the component. Right click on them and select "Create Component".)8. Open the interactive view of the component and explore by selecting edges from the network. Corresponding entries will be displayed on the table view. You can addannotations to the entries by editing the table.9. Save the selection results to Excel by executing the Excel Writer (XLS) node. Activity I:1: Use a File Reader node to read the file 9606.high.confidence.protein.links.v11.0.txt.gz located under the data folder parallel to the Exercises folder. (Hint: Drag anddrop the file to the workflow)2: Use a Row Filter node to limit the PPI network to the two receptors (5-HT(5A) and 5-HT(2B)). Their corresponding Ensemble IDs are ENSP00000258400 andENSP00000287907 respectively. Use the column protein1 for filtering. (Hint: use a regular expression in the form A|B to match multiple search terms.)3. Get the PDB ids of proteins form the output of the row filter node marked (PDB IDs) using the provided Joiner Node. Use protein2 and Ensembl ID as joining columns.Keep only the ID column from the second table.4. Connect the joined result to the PDB Data Extractor component which can be dragged and dropped from the KNIME Hub (https://kni.me/c/9el1UpNYGvoQx3UD). In thecomponent configuration dialog select ID column as the source of PDB IDs5. Use a String to Number node to convert chainLength and molecularWeight columns to numeric data type6. Search the Data Explorer node in the KNIME Hub (hub.knime.com) and drag and drop it and then connect it to the output of String to Number. Use the interactive viewof the node to have a closer look at the retrieved data (Hint: Follow the popup instructions to install the extension containing this node.) Exercise I: Protein-Protein Interactions in KNIMEProteins exhibit their function via interactions with other proteins in the body. In this exercise, we will investigate the protein-protein interactions (PPI) of two 5-Hydroxytryptamine (serotonin) receptors (5-HT(5A) and 5-HT(2B)) together. We will be using a PPI network downloaded from the online database STRING (https://string-db.org/). You will be provided with a file containing PPI network filtered for homo sapiens and containing only high confidence interactions (combined score > 900). Filter Protein of InterestAliases PDB IDsPPIWrite the filtered resultsto filePPIFilter Protein of InterestPDB IDsAliasesPDB Data Extractor Joiner Row Filter String To Number Data Explorer Column Rename File Reader Row Filter File Reader Excel Writer (XLS) Component File Reader Row Filter Joiner Column Rename Row Filter File Reader Activity II: Network Creation and Visualization1. Start by executing the provided Visualization Property Extractor node.2. On the configuration dialog of the provided Object Inserter node, set Node id column = protein1, Second node id column = protein2 and Edge id column = <RowID>.On the advanced options tab set Node partition column = protein1.3. Similarly, configure the Feature Inserter node with: Node id column = protein2, Name=Color, Value column = color and Type = based on value column4. Connect a Network Viewer node to the Feature Inserter node and configure it as follows: Layout Settings => Layout = cose and Node Settings => Fill color = color5. Connect the output of the Table Editor node to the second input port of the Network Viewer node.6. Connect an Excel Writer (XLS) node to the output of the provided Row Filter node and configure it by providing a file location.7. Create a component containing the nodes starting from Cleanup metanode to the Network Viewer and Row Filter nodes (excluding the Excel Writer (XLS) node). (Hint: To create a component, select the nodes to be included in the component. Right click on them and select "Create Component".)8. Open the interactive view of the component and explore by selecting edges from the network. Corresponding entries will be displayed on the table view. You can addannotations to the entries by editing the table.9. Save the selection results to Excel by executing the Excel Writer (XLS) node. Activity I:1: Use a File Reader node to read the file 9606.high.confidence.protein.links.v11.0.txt.gz located under the data folder parallel to the Exercises folder. (Hint: Drag anddrop the file to the workflow)2: Use a Row Filter node to limit the PPI network to the two receptors (5-HT(5A) and 5-HT(2B)). Their corresponding Ensemble IDs are ENSP00000258400 andENSP00000287907 respectively. Use the column protein1 for filtering. (Hint: use a regular expression in the form A|B to match multiple search terms.)3. Get the PDB ids of proteins form the output of the row filter node marked (PDB IDs) using the provided Joiner Node. Use protein2 and Ensembl ID as joining columns.Keep only the ID column from the second table.4. Connect the joined result to the PDB Data Extractor component which can be dragged and dropped from the KNIME Hub (https://kni.me/c/9el1UpNYGvoQx3UD). In thecomponent configuration dialog select ID column as the source of PDB IDs5. Use a String to Number node to convert chainLength and molecularWeight columns to numeric data type6. Search the Data Explorer node in the KNIME Hub (hub.knime.com) and drag and drop it and then connect it to the output of String to Number. Use the interactive viewof the node to have a closer look at the retrieved data (Hint: Follow the popup instructions to install the extension containing this node.) Exercise I: Protein-Protein Interactions in KNIMEProteins exhibit their function via interactions with other proteins in the body. In this exercise, we will investigate the protein-protein interactions (PPI) of two 5-Hydroxytryptamine (serotonin) receptors (5-HT(5A) and 5-HT(2B)) together. We will be using a PPI network downloaded from the online database STRING (https://string-db.org/). You will be provided with a file containing PPI network filtered for homo sapiens and containing only high confidence interactions (combined score > 900). Filter Protein of InterestAliases PDB IDsPPIWrite the filtered resultsto filePPIFilter Protein of InterestPDB IDsAliasesPDB Data Extractor Joiner Row Filter String To Number Data Explorer Column Rename File Reader Row Filter File Reader Excel Writer (XLS) Component File Reader Row Filter Joiner Column Rename Row Filter File Reader

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Created by: jeany
Created at: 2018-07-03
On NodePit since: 2020-12-17
Last update: 2024-04-18
Created with KNIME version: v4.1.3

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