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Related Concept Videos

Interactions Between Signaling Pathways01:19

Interactions Between Signaling Pathways

Signaling cascades usually lack linearity. Multiple pathways interact and regulate one another, allowing cells to integrate and respond to diverse environmental stimuli.
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Related Experiment Video

Updated: May 10, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

The UCSC Interaction Browser: multidimensional data views in pathway context.

Christopher K Wong1, Charles J Vaske, Sam Ng

  • 1Biomolecular Engineering Department, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.

Nucleic Acids Research
|June 11, 2013
PubMed
Summary
This summary is machine-generated.

The UCSC Interaction Browser integrates multiple high-throughput biological datasets, including gene expression and interaction data, for cancer research. This tool aids biologists in analyzing functional relationships and uncovering disease insights.

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Last Updated: May 10, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
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Published on: February 8, 2017

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
05:01

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Genomics

Background:

  • High-throughput biological data, including protein-protein interactions, protein-DNA interactions, and gene expression data, are increasingly available for model systems, particularly human cancer samples.
  • Analyzing these complex datasets to understand functional relationships between biological entities presents a significant challenge for researchers.

Purpose of the Study:

  • To introduce the University of California, Santa Cruz (UCSC) Interaction Browser, an online tool designed for the simultaneous visualization and analysis of diverse high-throughput biological datasets.
  • To provide biologists with a platform to explore functional relationships and gain insights into normal and disease processes through integrative network analysis.

Main Methods:

  • The UCSC Interaction Browser allows users to access public interaction networks and functional genomics data, as well as upload their own data for analysis.
  • It employs a novel visualization technique called CircleMap to simultaneously view multiple 'omics' datasets within the context of regulatory interactions (curated, predicted, directed, and undirected).

Main Results:

  • The browser facilitates navigation through correlative relationships for specific gene sets within biological pathways via a standard web browser.
  • It enables the integrative viewing of biological networks by consolidating information from various sources, offering a consensus view of gene and product interactions.

Conclusions:

  • The UCSC Interaction Browser provides a powerful, integrative platform for visualizing and analyzing complex biological networks and multi-omics data.
  • This approach can reveal novel insights into biological processes and disease mechanisms that may not be apparent from analyzing individual datasets in isolation.