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10_​Disease_​Genes

Disease Genes

This workflow highlights the functionality of KNIME for exploring, analyzing, and visualizing life science data related to diseases.

For a disease, 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 genes were 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 node degree (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 are subsequently 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 then presented in a tag cloud.

Right click the components and select "Execute and Open Views".
To save your in-view interaction use "Apply" and "Close" in the View lower right corner.
To open a component: Right click > Component > Open

This same workflow can be executed on the KNIME WebPortal as a remotely accessible guided analytics application.


This workflow highlights interactive data views in KNIME Analytics Platform to explore and visualize disease-related molecular data. To interact with the application open the Component Views in sequence and perform your selections. Data Preparation- Disease-Gene Annotations downloaded from Biomart andfiltered for OMIM data- Protein-Protein Interaction Data from STRING Sunburst ChartSunburst chart of disease, associated genesand 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 This workflow highlights interactive data views in KNIME Analytics Platform to explore and visualize disease-related molecular data. To interact with the application open the Component Views in sequence and perform your selections. Data Preparation- Disease-Gene Annotations downloaded from Biomart andfiltered for OMIM data- Protein-Protein Interaction Data from STRING Sunburst ChartSunburst chart of disease, associated genesand 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

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: jeany
Created at: 2017-11-16
On NodePit since: 2025-05-24
Last update: 2025-05-24
Created with KNIME version: v4.1.2
Tags: biologydiseasegenestag cloudPubMedbiomedicalOMIMNetwork ViewPubMedQuerySunburstguided analyticsnetwork viewLife sciences

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