AffyExonArray

Introduction

The Affymetrix Exon 1.0 array provides one or more probesets that probe the each exon (and sometimes introns and UTRs) of mammalian genes, with 1 to four probes per probeset. In addition to known genes and exons, potential genes and exons predicted by various algorithms are also probed. This array type is currently available for human, mouse and rat genomes. Probesets are divided by Affymetrix into three classes; core, extended and full. Relative to previous generation 3' biased arrays, the method of cDNA preparation and amplification is relatively unbiased.

AltAnalyze Supported Analyses

AltAnalyze allows users to select exon array CEL files or pre-normalized expression files to summarize gene expression levels (Ensembl genes), select probesets for analysis (modified core, extended and full sets), identify alternative exons (e.g., FIRMA, splicing-index, MiDAS), annotate these exons in the context of splicing annotations (e.g., alternative-splice sites, intron retention) and assess the functional impact of alternative exon expression (e.g., associated proteins, domains, miRNA binding sites). Along with exon arrays, gene arrays (Affymetrix Gene 1.0) can be analyzed using these same methods. Over-representation of pathways, GO-terms, domains/motifs and miRNA binding sites is also supported. These results can be examined in the produced spreadsheets or visualized in the associated software DomainGraph.