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  • 07_Gene_Expression_Analysis
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Gene Expression Analysis

Life Sciences Bioinformatics R Shared components Interactive views

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In this workflow, we analyze RNA-Seq data from tumors and matched normal tissue from three patients with oral squamous cell carcinomas (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009317). Differentially expressed genes are discovered using the R package edgeR and are then displayed in an interactive view. Subsequently, genes are hierarchically clustered based on their expression pattern, and the results are shown via a dendrogram alongside a heatmap. We then perform a pathway enrichment analysis and look for compounds targeting the gene product of interest.

External resources

  • Analzying Gene Expression Data with KNIME

Used extensions & nodes

Created with KNIME Analytics Platform version 4.1.2
  • KNIME Base Chemistry Types & Nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.1

  • KNIME BigQuery Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

  • KNIME Core Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.2

  • KNIME Database Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.1

  • KNIME Distance Matrix Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.1

  • KNIME Expressions Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

  • KNIME Interactive R Statistics Integration Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.1

  • KNIME JavaScript Views Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.2

  • KNIME JavaScript Views (Labs) Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

  • KNIME JSON-Processing Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

  • KNIME Math Expression (JEP) Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

  • KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.2

  • KNIME REST Client Extension Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.1

  • KNIME SVG Support Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

  • KNIME Virtual Nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.1.0

  • RDKit KNIME integration Trusted extension

    NIBR

    Version 4.0.1

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License (CC-BY-4.0)
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