Whole-Transcript Gene Expression &
Alternative Splicing

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See the Whole Gene Expression Picture-Accurately and Precisely

By enabling you to interrogate the entire length of the gene and not just the 3' end, Affymetrix GeneChip® Exon and Gene Arrays offer a more complete and accurate picture of overall gene expression than traditional 3'-based expression arrays. Powered by the unbiased whole-transcript assay, Exon and Gene 1.0 ST Arrays allow you to distinguish between different transcript isoforms and detect transcripts that you would miss using 3'-biased approaches.

See the real biology

Real biology happens at the transcript level, not the gene level
Whole Transcript Expression and Alternative Splicing: Exon 1.0 ST Arrays

With approximately four probes per exon and roughly 40 probes per gene, the GeneChip® Exon 1.0 ST Array is the most powerful and comprehensive expression array on the market. Exon array enables unbiased measurement across the length of the gene allowing you to detect transcripts that would be missed with 3' arrays. Detect exon- and gene-level expression and alternative splicing events from single experiment.
With approximately four probes per exon and roughly 40 probes per gene, the GeneChip® Exon 1.0 ST Array is the most powerful and comprehensive expression array on the market. Exon array enables unbiased measurement across the length of the gene allowing you to detect transcripts that would be missed with 3' arrays. Detect exon- and gene-level expression and alternative splicing events from single experiment.
Figure 1
With approximately four probes per exon and roughly 40 probes per gene, the GeneChip® Exon 1.0 ST Array is the most powerful and comprehensive expression array on the market. Exon array enables unbiased measurement across the length of the gene allowing you to detect transcripts that would be missed with 3' arrays. Detect exon- and gene-level expression and alternative splicing events from single experiment.
With approximately four probes per exon and roughly 40 probes per gene, the GeneChip® Exon 1.0 ST Array is the most powerful and comprehensive expression array on the market. Exon array enables unbiased measurement across the length of the gene allowing you to detect transcripts that would be missed with 3' arrays. Detect exon- and gene-level expression and alternative splicing events from single experiment.

GeneChip® Exon Arrays provide the most comprehensive coverage of the genome and enable two complementary levels of analysis-gene expression and alternative splicing. Multiple probes per exon enable “exon-level” analysis, which allows you to distinguish between different isoforms of a gene. This exon-level analysis on a whole-genome scale opens the door to detecting specific alternative splicing events that may play a central role in disease mechanism and etiology. You can also perform “gene-level” analysis, in which multiple probes on different exons are summarized into a single expression value of all transcripts from the same gene, enabling similar analysis workflows to 3'-based gene expression.

See the whole gene

Measure expression using the entire gene instead of just the 3'
Whole Transcript Expression: Gene 1.0 ST Arrays

The Gene 1.0 ST Array System offers a powerful solution for whole-genome, whole-transcript expression analysis for human, mouse and rat. Each of the well-annotated genes is represented by approximately 26 probes spread across the full length of the gene, providing a more complete and accurate picture of gene expression than 3'-based expression array designs.
The Gene 1.0 ST Array System offers a powerful solution for whole-genome, whole-transcript expression analysis for human, mouse and rat. Each of the well-annotated genes is represented by approximately 26 probes spread across the full length of the gene, providing a more complete and accurate picture of gene expression than 3'-based expression array designs.
Figure 2
The Gene 1.0 ST Array System offers a powerful solution for whole-genome, whole-transcript expression analysis for human, mouse and rat. Each of the well-annotated genes is represented by approximately 26 probes spread across the full length of the gene, providing a more complete and accurate picture of gene expression than 3'-based expression array designs.
The Gene 1.0 ST Array System offers a powerful solution for whole-genome, whole-transcript expression analysis for human, mouse and rat. Each of the well-annotated genes is represented by approximately 26 probes spread across the full length of the gene, providing a more complete and accurate picture of gene expression than 3'-based expression array designs.

The Gene 1.0 ST Array System offers a cost-effective solution for whole-genome, whole-transcript expression analysis for human, mouse and rat. Each of the well-annotated genes is represented by approximately 26 probes spread across the full length of the gene, providing a more complete and accurate picture of gene expression than 3'-based expression array designs. All 26 probes are automatically summarized into a single expression value per gene, which means you can use standard analysis software packages and simple analysis workflows to analyze data. Gene 1.0 ST Arrays are the most advanced and cost-effective gene expression profiling option for new microarray users.

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GeneChip® Exon 1.0 ST Array System for Human, Mouse and Rat

The Exon 1.0 ST Array System is part of a complete solution that enables whole-genome, gene-level expression and alternative splicing studies. GeneChip® Exon Arrays provide the most comprehensive coverage of the genome, including empirically supported and predicted transcribed sequences, enabling the discovery of previously unidentified novel events.

GeneChip® Gene 1.0 ST Array System for Human, Mouse and Rat

The Gene 1.0 ST Array is part of a complete solution for gene expression analysis that enables whole-genome, gene-level expression studies for well-characterized genes. The array contains the most up-to-date content of well-annotated genes, and data is analyzed using a simple workflow.

Affymetrix Expression Console™ Software

Expression Console™ software supports probe-set summarization and CHP file generation for GeneChip® Gene and Exon Arrays, as well as 3' expression arrays. The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms. The algorithms offered include:

  • MAS5 Statistical algorithm
  • Probe Logarithmic Intensity Error Estimation (PLIER)
  • Robust Multichip Analysis (RMA)

GeneChip-Compatible™ Software

For advanced secondary analysis, several GeneChip-Compatible™ software packages are available for both gene- and exon-level analysis.

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Exon-level integration of proteomics and microarray data

Presented by Crispin Miller, Ph.D., Paterson Institute for Cancer Research, Manchester, UK

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Affymetrix Exon Arrays Reveal Complexity of the Human Transcriptome

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Discovery of Novel Splice Variations Improves Glial Tumor Classification

Erasmus Medical Center's Pim French and Justine Peeters talk with Noam Shomron at MIT about using exon arrays to study alternative splicing in glioma

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Researchers Develop Improved Molecular Classification System for Rare Childhood Cancer

Dr. Timothy Triche of Childrens Hospital Los Angeles talks about using gene expression profiles to provide safer, more effective treatments

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Demonstration of Partek Genomics Suite™ for the Analysis of GeneChip® Exon Arrays

Tom Downey, President and Data Analysis Consultant at Partek®, Inc.

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Demonstration of Biotique Systems' XRAY for the Analysis of GeneChip® Exon Arrays

Presented by Biotique Systems' John Burke

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Publications and References:

Publications and References for Affymetrix® GeneChip® Exon and Gene Arrays

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