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10_​Disease_​Genes

Workflow

Disease Genes
biologydiseasegenestag cloud
DiseaseGenes This workflow highlights interactive data views in KNIME Analytics Platform to explore and visualize disease-related molecular data. For a disease of interest, such as Maple Syrup Urine Disease, the associated genes in the OMIM database are displayed in a sunburst chart. Moreover, interactions of the proteins encoded by the disease-associated geneswere shown in the same chart. Then, the network of disease genes and their interaction partners are displayed. The next step reveals the network of disease genes and their interaction partners. One can filter the nodedegree (the number of connections a node has to other nodes) using a range slider. Information about the nodes themselves is also displayed in the table below. Selected genes in the network or in the table aresubsequently used to query information from the biomedical literature that is stored in the database PubMed. The titles and abstracts of the resulting papers are displayed. Frequent terms in these documents are thenpresented in a tag cloud.Launching the workflow from the WebPortal displays the same interactive views onto a web page.BLOG: https://www.knime.com/blog/a-yummy-way-to-explore-life-science-data Data Preparation- Disease-Gene Annotations downloaded from Biomartand filtered for OMIM data- Protein-Protein Interaction Data from STRING Sunburst ChartSunburst Chart of disease, associatedgenes and interaction partners Interaction NetworkNetwork of disease genes and interactionpartners PubMed QueryDisplays title and abstract of extracted documents andtag cloud of frequent terms in the documents Sunburst DiseaseName_input InvestigateNetwork DataPrep PubMedQuery Input_PubMedQuery DiseaseGenes This workflow highlights interactive data views in KNIME Analytics Platform to explore and visualize disease-related molecular data. For a disease of interest, such as Maple Syrup Urine Disease, the associated genes in the OMIM database are displayed in a sunburst chart. Moreover, interactions of the proteins encoded by the disease-associated geneswere shown in the same chart. Then, the network of disease genes and their interaction partners are displayed. The next step reveals the network of disease genes and their interaction partners. One can filter the nodedegree (the number of connections a node has to other nodes) using a range slider. Information about the nodes themselves is also displayed in the table below. Selected genes in the network or in the table aresubsequently used to query information from the biomedical literature that is stored in the database PubMed. The titles and abstracts of the resulting papers are displayed. Frequent terms in these documents are thenpresented in a tag cloud.Launching the workflow from the WebPortal displays the same interactive views onto a web page.BLOG: https://www.knime.com/blog/a-yummy-way-to-explore-life-science-data Data Preparation- Disease-Gene Annotations downloaded from Biomartand filtered for OMIM data- Protein-Protein Interaction Data from STRING Sunburst ChartSunburst Chart of disease, associatedgenes and interaction partners Interaction NetworkNetwork of disease genes and interactionpartners PubMed QueryDisplays title and abstract of extracted documents andtag cloud of frequent terms in the documents Sunburst DiseaseName_input InvestigateNetwork DataPrep PubMedQuery Input_PubMedQuery

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Nodes

10_​Disease_​Genes consists of the following 84 nodes(s):

Plugins

10_​Disease_​Genes contains nodes provided by the following 8 plugin(s):