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User's Manualsdd
 
  • ArrayFusion Step-by-Step Quick Guide 
    		•   first time visit?
  • Affymetrix Integrated Genome Browser User's Guide
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  • Upload GFF files into GBrowser
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    Input Formats
     
    Cytological Location
  • 9p21.3  (a single band)
  • 9p21  (a single band from the range of 9p21.3, 9p21.2 and 9p21.1)
  • 9p13-p21  (a range)
  • 9pter-p21  (a range from the end of p arm)
  • 9q21-qter  (a range to the end of q arm)
  • 9q21-qter or 9q21-9qter  (either way)

    • GenBank and/or RefSeq mRNA Accession  (support combination queries)
  • NM_006848  (RefSeq mRNA Accession)
  • BC008796  (GenBank Accession)
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    Output Columns in TXT Annotations
     
    1. Gene Symbol
    1.1 Approved Symbol, Previous Symbols or Aliases?
    Query HGNC ID Approved Symbol Approved Name Status Previous Symbols Aliases  ...  RefSeq IDs RefSeq (mapped data)
        1st     2nd 3rd      
    (ArrayFusion searches sequentially until the corresponding gene symbol is matched, no matter what the users request)

    1.2 Map Gene Symbols to Affymetrix HG-U133 Plus 2.0 Probesets by 'Approved Symbol'
    Query HGNC ID HG-U133_Plus_2 Probesets Approved Symbol Approved Name Status Previous Symbols Aliases  ...  RefSeq IDs RefSeq (mapped data)
    ADORA2A   1556669_a_at, 205013_s_at ADORA2A              
    CX50 (Aliases)   208489_at GJA8       CX50      
    (user queried 'CX50', but ArrayFusion uses 'GJA8' to do the mapping)

    1.3 Map Gene Symbols to Genomic Coordinates
    Query HGNC ID Approved Symbol Approved Name Status Previous Symbols Aliases  ...  RefSeq IDs RefSeq (mapped data)
                    1st 2nd
    (will use 'RefSeq IDs' first, if it is empty then 'RefSeq (mapped data)')

    2. Affymetrix Human Exon 1.0 ST Array
    2.1 Probeset Annotations
    Probeset ID Seqname Strand Start Stop Probe Count Transcript Cluster ID Exon ID PSR ID Gene Assignment Level
    2315102                 A1 // A2 /// B1 // B2  
    (Columns in NetAffx annotations)
     
    Probeset ID Seqname Strand Start Stop Probe Count Transcript Cluster ID Exon ID PSR ID Accession Gene Symbol Level
    2315102                 A1 A2  
    2315102                 B1 B2  
    (ArrayFusion splits 'Gene Assignment into separate and handy columns)

    2.2 Transcript Cluster Annotations
    Transcript Cluster ID Seqname Strand Start Stop Total Probes Gene Assignment
    2315100           A1 // A2 // A3 // A4 // A5 /// B1 // B2 // B3 // B4 // B5
     
    Transcript Cluster ID Seqname Strand Start Stop Total Probes Accession Gene Symbol Gene Title Cytoband Entrez Gene ID
    2315100           A1 A2 A3 A4 A5
    2315100           B1 B2 B3 B4 B5
    (same as above)

    Assembly Conversions
     
    This feature is for reference only, since the converted coordinates sometimes cannot represent the probesets per se like the first example as shown below. We noticed that some of the alignments are different between UCSC and NetAffx in build 35 (e.g. 1438_at).
     
    Probeset 1438_at
  • chr3:185762717-185782104  (19387 bp, NetAffx annotation NCBI 36)
  • chr3:185762717-185782104  (19387 bp, UCSC affyU133Plus2 NCBI 36)
    •  
  • chr3:185762725-185782112  (19387 bp, ArrayFusion LiftOver, convert from NCBI 36 to 35)
  • chr3:185762725-185782112  (19387 bp, UCSC LiftOver output, convert from NCBI 36 to 35)
    •  
  • chr3:185771805-185782112  (10307 bp, NetAffx annotation NCBI 35)
  • chr3:185762725-185782112  (19387 bp, UCSC affyU133Plus2 NCBI 35)
    •  
    And the second example, the alignments between build 35 and 36 are sometimes different due to the improvement of the assembly (e.g. 1552643_at). We have informed UCSC and Affymetix in terms of this issue.
    Probeset 1552643_at
  • chr19:20619832-20636242  (16410 bp, NetAffx annotation NCBI 36)
  • chr19:20619832-20636242  (16410 bp, UCSC affyU133Plus2 NCBI 36)
    •  
  • chr19:20619832-20636242  (16410 bp, ArrayFusion LiftOver, convert from NCBI 36 to 35)
  • chr19:20619832-20636242  (16410 bp, UCSC LiftOver output, convert from NCBI 36 to 35)
    •  
  • chr19:20619832-20621052  (1220 bp, NetAffx annotation NCBI 35)
  • chr19:20619832-20621052  (1220 bp, UCSC affyU133Plus2 NCBI 35)
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    Services & Applications
    ArrayFusion 1.5.7
    SET 1.0.3
    easyExon 1.0.4
    MFSelector 1.0.0



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