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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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,...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
What is Gene Expression?01:36

What is Gene Expression?

A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised  of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...

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Expander: from expression microarrays to networks and functions.

Igor Ulitsky1, Adi Maron-Katz, Seagull Shavit

  • 1Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel.

Nature Protocols
|February 6, 2010
PubMed
Summary
This summary is machine-generated.

Expander software simplifies gene expression microarray data analysis, enabling efficient normalization, clustering, and network inference for biological insights. This integrated platform supports the full analysis pipeline from raw data to regulatory networks.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Gene expression microarray data analysis presents challenges in extracting meaningful biological knowledge from large datasets.
  • Integrated software platforms are needed to streamline the complex process of microarray data analysis.

Purpose of the Study:

  • To present Expander (EXPression ANalyzer and DisplayER), an integrated software platform for comprehensive microarray data analysis.
  • To detail a protocol for utilizing Expander 5.0 for tasks ranging from data normalization to transcriptional regulatory network inference.

Main Methods:

  • The protocol involves importing raw microarray data into Expander 5.0.
  • Data undergoes normalization, filtering, clustering, and network-based analyses.
  • Gene groups are evaluated for functional enrichment (Gene Ontology), co-regulation (transcription factor and microRNA targets), and co-location.

Main Results:

  • Expander 5.0 facilitates a complete microarray analysis protocol.
  • The software allows for visualization of results at each analysis step.
  • The entire analysis protocol can be executed within approximately one hour.

Conclusions:

  • Expander provides a user-friendly, integrated solution for gene expression microarray data analysis.
  • The platform supports diverse analytical approaches, including functional enrichment and network inference.
  • Expander significantly reduces the time and complexity associated with extracting biological knowledge from microarray data.