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A Pearson's correlation test was used to compare our mean tag expression values to the recent RNA-seq data of Hampton et al. (2013), who identified 2,083/14,573 distinct transcripts differentially expressed among October, torpid, interbout-aroused and April 13-lined ground squirrels.
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Due to the low level of technical variation between cleaned and uncleaned FANG-1 samples, differential gene expression analysis used the mean tag count values for cleaned and uncleaned FANG-1 samples for each enrichment method.
The averaged binned gene expression values were then graphed against mean tag counts for each bin.
When the data was then filtered for tags meeting the criteria ⩽0.5 mean tag count in normal brain but >2 tags in ependymoma, the uncharacterised gene C1orf192 showed the highest difference in expression of 17.3 (Table 3).
Y-axes: mean tag density.
PH, SB, FP and EE participated in tag expression confirmation and SAGE tag annotation.
Tag expression begins at approximately 10 weeks of age.
In the present study, ~ 17% of the transcripts that provide tags (mean expression of ≥1TPM [tags per million] from at least 4 replicates) were found to be derived from the antisense strand of genes.
The gene-wise expression values from different samples were combined by computing the mean tags per million value.
Tagging quality was generally good (mean tagging score 3.7 4.5) (Fig. 3).
(D ) Line plots of EDGE-tag expression patterns for all 2,159 significant differentially expressed tags; mean scaled counts, solid line, ±SEM, dotted line.
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