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To match non-exonic TARs to rice Unigenes (sets of transcript sequences derived from the same transcription unit), which were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/UniGene/UGOrg.cgi TAXID = 4530), a cutoff of E≤e−10 was used.
* UniGene is a database of sets of transcript sequences that appear to come from the same transcription locus.
A search on the NCBI UniGene database [ 72] that provides information on sets of transcript sequences that appear to come from the same transcription locus was performed to ascertain redundancy and group identified transcripts.
Based on information in the UniGene database that provides sets of transcript sequences that appear to come from the same transcription locus, these mRNA sequences with similar signal sequence were placed in 27 distinct UniGene entries (Table 2).
Since both UniGene and RefSeq are billed as non-redundant sets of transcript IDs, and have been used in prior studies with mixed results, it is still unclear as to which approach is better.
The UniGene database contains an extensive collection of information about sets of transcript sequences, including ESTs (Expressed Sequence Tags).
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A list of 8462 sets of transcripts sharing a particular Gene Ontology term was generated by considering.
However, when we combined the TaqMan and microarray data, we observed that the sets of transcripts that correlated with TCF7L2 expression significantly overlapped with the set of transcripts that correlated with GAPDH and B2M expression.
Clearly, many genes (thus many sets of transcripts) contain target sites that fall into more than one of these situations.
The pathway enrichment analysis on sets of transcripts with significant correlations was performed using the Panther Classification System [27].
Vaccine-exposed GL26 (GL26B6V) similarly clustered away from other GL26 sublines on PCA using analogous sets of transcripts (Fig. 1A).
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