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We have defined 33,737 retina transcript clusters (RTCs) as single units with non-redundant sequences, although multiple transcript clusters can be in the same UniGene cluster.
In cases where multiple transcript clusters mapped to the same gene, we calculated gene expression as the median of all corresponding transcript clusters.
Lastly, we reduced the effect of inaccurate annotations by removing transcript clusters with more than one annotated Entrez Gene identifiers as well as multiple transcript clusters annotated by the same Entrez Gene identifier.
Early attempts at characterizing the Drosophila Pgk identified at least three different electrophoretic variants (Chew and Cooper 1973), and subsequent studies using RNase protection assay and primer extension found multiple transcript clusters (Roselli-Rehfuss et al. 1992).
Under the most stringent clustering criterion (95% amino acid identity over 95% of the length of both sequences), 675 of 695 protein sequences did not group with any other sequence, and only 9 multiple transcript clusters occurred, with the largest containing 3 members.
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These multiple transcript unigene clusters can represent transcription variants, allelic variants, closely related paralogues, misassembled transcripts, or transcripts that were fragmented due to low coverage.
If a gene had multiple transcripts we clustered all exons from all transcripts into one super-transcript.
A parallel analysis identified 2105 unique transcript clusters as differentially expressed (after multiple test correction) during the seven days of lymphocyte stimulation compared to D0.
The splice-variant ANOVA exploring alternate exon usage changes over time identified 658 transcript clusters with alternate exon usage after multiple test correction (q-value < 0.0001).
In total, 2176 protein-coding genes containing multiple TSSs were identified and matched to exon array core transcript clusters by gene symbol of which 2036 genes had available exon expression data.
Each cluster of PASA alignment assemblies can contain either single or multiple transcript alignment assemblies.
Related(12)
many transcript clusters
several transcript clusters
multiple transcript sites
multiple receptor clusters
multiple transcript variants
multiple transcript probes
multiple transcript forms
multiple transcript fragments
multiple transcript intensities
multiple gene clusters
multiple transcript sequences
multiple transcript profiles
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