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Most of the inconsistent transcripts exhibit only minor changes in relative expression levels (~10%to20%0% increase or decrease) and relatively insignificant p values.
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The sample with inconsistent chimeric transcript expression was 2.7 cm in its largest dimension, and the chimeric transcript negative tumour was 2.5 cm in its largest dimension.
Part of this inconsistent regulation of transcripts and proteins is explainable by known regulation mechanisms.
The same inconsistent regulation of transcripts annotated as raffinose synthase [ 54] or as galactinol-sucrose galactosyltransferase in the RefSeq [ 55] annotation was observed: VIT_17s0000g08960 was allocated to cluster 2 thus induced by stress at several stages whereas VIT_14s0066g00810 was assigned to cluster 1 exhibiting tendencies of down-regulation.
After removing these, 7 of 2841 calls (0.24%) located in seven different transcripts remain inconsistent.
This number may be an underestimate since results for one patient were inconsistent for all 6 transcripts.
The other group includes the remaining 4118 transcripts with inconsistent sequence similarity along the gene body and flanking regions.
MCL led to retention of more orthologs than reciprocal BLAST because transcripts with inconsistent reciprocal matches between species were now retained as part of a larger cluster.
Fewer than 4% of the transcripts show inconsistent sign changes (i.e. under expressed in BG01V APCs and over expressed in CCF-STTG1 cells relative to H9 APCs or over expressed in BG01V APCs and under expressed in CCF-STTG1 cells relative to H9 APCs).
Also inconsistent with already reported transcript profiles [ 19] we identifed a downregulation of several molecules involved in innate immune responses, such as Toll-like receptor 2, IL-1 receptor-associated kinase (IRAK3), IL-1 and its receptor in our SAA patient pools.
We removed transcripts that were inconsistent between Baek et al. [ 24] and current human annotation.
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