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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Related Experiment Video

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

Graphite Web: Web tool for gene set analysis exploiting pathway topology.

Gabriele Sales1, Enrica Calura, Paolo Martini

  • 1Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy.

Nucleic Acids Research
|May 14, 2013
PubMed
Summary

Graphite web offers a novel, user-friendly platform for pathway and network analysis of gene expression data. It integrates advanced topological and multivariate methods with interactive visualizations, simplifying complex biological data interpretation for researchers.

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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Gene expression data analysis is complex, often relying on univariate or non-topological methods that overlook gene relationships.
  • Existing topological and multivariate pathway analyses are powerful but require significant bioinformatics expertise, limiting accessibility.
  • Biological pathways are best represented as networks, incorporating both gene lists and their interconnections.

Purpose of the Study:

  • To introduce Graphite web, a novel web server for pathway and network analysis of gene expression data.
  • To provide an accessible tool that combines topological and multivariate pathway analyses with interactive network visualizations.
  • To facilitate easier interpretation of complex gene expression results for a broader research community.

Main Methods:

  • Development of a web server implementing five distinct gene set analyses.
  • Integration of topological and multivariate pathway analysis approaches.
  • Inclusion of interactive network visualization tools for results interpretation.
  • Support for gene expression data from microarray and RNA-seq experiments across three model organisms and two pathway databases.

Main Results:

  • Graphite web is presented as the first public web server offering combined topological and multivariate pathway analyses.
  • The tool features an efficient system for interactive network visualizations to aid in understanding results.
  • It supports analysis across multiple organisms and pathway databases, enhancing its utility.

Conclusions:

  • Graphite web democratizes advanced pathway analysis by merging powerful methods with user-friendly visualization.
  • The platform simplifies the interpretation of complex gene expression data, bridging the gap between bioinformatics and biological research.
  • This tool is freely available, promoting wider adoption and advancing biological data interpretation.