title: GNF1H
status: Public on Mar 19 2004
contact.city: San Diego
contact.first: John
contact.last: Walker
contact.email: jwalkergnf@gmail.com, john.walker@novartis.com
contact.state: CA
contact.address: 10675 John Jay Hopkins Dr
contact.country: USA
contact.institute: NIBR
organism: Homo sapiens
description: GNF1H
  In 2002, we identified a non-redundant set of human target sequences using the following sources: RefSeq (15,491 sequences), Celera (49,859 sequences), and Ensembl (33,698 sequences). First, all sequences were RepeatMasked to remove repetitive elements. Next, sequence identity between individual sequences was established using pairwise BLAT or BLAST and sim4. The results from single-linkage clustering were further triaged to produce a final target set of 44,775 targets with the highest degree of confidence of computational prediction (biasing toward sequences containing Interpro domains and away from non-coding RNAs). Finally, the human sequence set was pruned of all targets already represented on Affymetrix's commercially available U133A array, leaving 22,645 target sequences for our custom array. The final target sets were submitted to the Affymetrix's chip design pipeline for fabrication of the GNF1H arrays.
  
  Update: At the time of publication (2004, DOI: 10.1073/pnas.0400782101), by request from Celera, we have masked any and all sequences that were derived from Celera data. We have been able to re-annotate and associate 11,406 probe sets to public data, and for the rest (11,086 probe sets), we masked the sequences by poly-N and replaced their annotation if any with "predicted transcript (Celera)" and their target regions and individual probe sequences are all unavailable. For approximately 750 more probe sets, the annotation is based on the orthologous annotation data available in 2004 and the phrase "a predicted transcript (Celera), similar to :[insert the rest [e.g. M.musculus]]" should be implied. Caveat emptor: Even though all these sets are designed from human transcripts and computational predictions, it should not be expected that they are efficient to assay the modern version of any human transcript. All individual probe sequences for 11,406 sets are provided for the interested parties to do their own sequence analysis (suggested route: blast/blat or otherwise align individual probes to the most recent genome+transcriptome database and use a >8 out of 11 voting system to determine the most likely target(s)). Such analysis will be in most cases more precise than any precomputed annotation (however, in many cases this new, precise annotation will be "intergenic region", "intron", "antisense to :" - due to old age of the array probes may have been designed outside of the true UTR, the 2002 genomic sequence may have been misassembled, predictions were truncated or completely wrong etc).