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Table 1 PANTHER annotation versus disseminated annotation releases 1 & 2. The data from the Supplementary Files 1 & 2 were submitted to the PANTHER website either using the probe IDs or the gene IDs. The differences in identification, display, and absentee calls, between the datasets and the annotation releases are due to the fact that PANTHER is continuously updated, only considers protein coding genes, excludes GenBank-only annotated mRNAs, and retains only the gene ID with the highest suffix.

From: Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700™/Panther™ probe-to-gene annotations

   Number of unique entries ~
Annotation Version Probe ID/Gene ID set submitted found by PANTHER displayed by PANTHER not found by PANTHER not accounted for
V1 Probe ID 51 30 29 21 0
  Gene ID 51 44 22 2 5
V2 Probe ID 110 65 59 45 0
  Gene ID 110 98 44 0 12