Hub
WorkflowWorkflow

Gene Expression Analysis

Life Sciences Bioinformatics R Shared components Interactive views
KNIME profile image

Last edited: 

Drag & drop
Like
Download workflow
Copy short link
Workflow preview
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.

Used extensions & nodes

Created with KNIME Analytics Platform version 4.4.1 Note: Not all extensions may be displayed.
  • KNIME Base nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.1

    KNIME profile image
    knime
  • KNIME BigQuery Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.0

    KNIME profile image
    knime
  • KNIME Database Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.1

    KNIME profile image
    knime
  • KNIME Expressions Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.0

    KNIME profile image
    knime
  • KNIME Google Connectors Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.1

    KNIME profile image
    knime
  • KNIME Interactive R Statistics Integration Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.1

    KNIME profile image
    knime
  • KNIME JavaScript Views Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.1

    KNIME profile image
    knime
  • KNIME JavaScript Views (Labs) Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.0

    KNIME profile image
    knime
  • KNIME Javasnippet Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.1

    KNIME profile image
    knime
  • KNIME JSON-Processing Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.1

    KNIME profile image
    knime
  • KNIME Math Expression (JEP) Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.0

    KNIME profile image
    knime
  • KNIME Parallel Chunk Loop Nodes Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.0

    KNIME profile image
    knime
  • KNIME Quick Forms Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.1

    KNIME profile image
    knime
  • KNIME REST Client Extension Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.0

    KNIME profile image
    knime
  • KNIME SVG Support Trusted extension

    KNIME AG, Zurich, Switzerland

    Version 4.4.0

    KNIME profile image
    knime
  • RDKit Nodes Feature Trusted extension

    NIBR

    Version 4.3.0

    manuelschwarze
Loading deployments
Loading ad hoc executions
Discussion