ArrayFusion - a web application for multi-dimensional analysis of CGH, SNP and microarray data
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ArrayFusion annotates conventional CGH results and various types of microarray data from a range of platforms (cDNA, expression, exon, SNP, array-CGH and ChIP-on-chip) and converts them into standard formats which can be visualized in genome browsers (Affymetrix Integrated Genome Browser and GBrowse in the HapMap Project). Converted files can then be imported simultaneously into a single genome browser to benefit the collective interpretation between different array results. ArrayFusion therefore provides a new type of tool facilitating the integration of CGH and array results to provide new experimental directions.

Multi-dimensional Analysis
  • Batch convert probesets into EGR and/or GFF formats (for genome browsers).
  • Convert HGNC Gene Symbol to representative Affymetrix HG-U133 Plus 2.0 probesets.
  • Convert HGNC Gene Symbol to genome coordinates (by RefSeq mRNA Accessions).
  • Annotations
  • Batch query commercial probesets or public domain IDs.
  • Support between-chip orthologs for Affymetrix's expression arrays.
  • Convert Genome Coordinates between Assemblies
  • Convert between NCBI build 35 and 36; powdered by UCSC LiftOver's chain conversion files.

  • Supported Inputs
    Public Domain IDs
  • HGNC Gene Symbol
  • GenBank and RefSeq mRNA Accession
  • Ensembl Gene ID
  • Cytological Location
  • Expression Array Systems
  • Affymetrix Human, Rat, Mouse, C. elegans and Yeast Arrays
  • Agilent Human Oligo Microarrays
  • Exon Array Systems
  • Affymetrix Human Exon Arrays
  • SNP Array & Oligo aCGH Systems
  • Affymetrix Human Mapping Arrays
  • Agilent Human Genome CGH Microarrays
  • Tiling Array & ChIP-on-chip Systems
  • Agilent Human ChIP-on-chip Microarrays

    Output Formats
    Annotation Files
  • TXT tab-delimited annotations (open with spreadsheet programs)
  • File Formats for Genome Browsers
  • EGR format for Affymetrix Integrated Genome Browser
  • GFF format for The Generic Genome Browser, e.g. HapMap Public Data
  • Failure Files
  • Invalid query, empty alignments or deleted in new assembly
    Yang TP, Chang TY, Lin CH, Hsu MT, Wang HW. (2006). ArrayFusion: a web application for multi-dimensional analysis of CGH, SNP and microarray data. Bioinformatics 22(21):2697-2698. [PubMed Abstract]

    Services & Applications
    ArrayFusion 1.5.7
    SET 1.0.3
    easyExon 1.0.4
    MFSelector 1.0.0