GeneChip™ Human Genome U133 Plus 2.0 Array - FAQs

The probe interrogation position indicates the base position on the consensus/exemplar sequence where the central base of the probe aligns, which is the 13th base of a 25mer probe.

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The probes on the 3' IVT platform are in the sense orientation.

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Occasionally, it is not possible to select either a unique probe set or a probe set with all probes common among multiple transcripts ("_s_at" ). In such cases, similarity criteria are suspended, and the resulting probe set name is appended with the "_x_at" extension. These probe sets contain some probes that are identical, or highly similar, to unrelated sequences. These probes may cross-hybridize in an unpredictable manner with sequences other than the main target. Data generated from these probe sets should be interpreted with caution, due to the likelihood that some of the signal is from transcripts other than the one being intentionally measured.

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The primary goal in probe set selection is to select a probe set unique to a single transcript or common among a small set of similar transcript variants. A probe set name is appended with the "_s_at" extension when all the probes exactly match multiple transcripts. The probe set selection process generally favors probe sets measuring fewer transcripts. Probe sets with common probes among multiple transcripts (the "_s_at" probe sets), are frequent and are to be expected, due to alternative polyadenylation and alternative splicing. In most cases, "_s_at" probe sets represent transcripts from the same gene, but the same probe set can sometimes also represent transcripts from homologous genes. One transcript may be represented by both a unique and an "_s_at" probe set when the transcript variation is sufficient.

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The GeneChip Exon Arrays represent a new array design philosophy for the most comprehensive and informative coverage with the exon as the basic unit of expression analysis. Such an inclusive design enables discovery of new and novel splicing events not previously observed experimentally. Some of the key differences are summarized below using the human arrays as an example; refer to the “GeneChip Exon Array Design” Technical Note and the “Design and Performance of the GeneChip Human Genome U133 Plus 2.0 and Human Genome U133A 2.0 Array” Technical Note for more details.

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The majority of the HG-U133 Plus 2.0 Array consensus sequences are well covered in the new design with approximately 75% of them containing over 8 probes on the Exon Array. The remaining 25% have less overlap with the new exon probes, and are mostly attributed to EST-based HG-U133 Array probe sets that do not contain an annotated coding region. As a result, in many such cases, the entire HG-U133 Array EST-based consensus sequence is designated as one PSR, with around 4 probes selected for that entire region.

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Signal and detection values from the exon arrays cannot be directly compared to that of the HG-U133 arrays. Major differences in array design and assay prevent meaningful comparisons at the signal level. Splice variation and polyadenylation variation can confound comparisons at the biological level (i.e., direction of change) due to differences in probe placement and bias in the target preparation assays.

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