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The headings should be clarified or perhaps additional columns could be used for listing expression patterns.
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This table lists genes whose expression patterns are best explained by a synergistic relationship between the presence of AtxA and CO2.
Genes in this list can be further divided into two gene lists: high expression pattern correlated with poor survival and low expression pattern correlated with poor survival.
If the two miRNAs that had marginal correlation (p values between 0.05 and 0.07) was included (they could still be significant due to the use of different databases in this comparative study), total 77% of the miRNAs in our list had coherent expression patterns with their host genes.
In particular, transcripts belonging to the PKA signaling pathway, such as PDE3B, PDE4A and PDE4D phosphodiesterases, turned out to be the most overrepresented genes in such list, with differential expression patterns, which were confirmed also in the additional set of paired diagnosis-relapse BCR ABL1-positive ALL samples analyzed with Human Exon 1.0 ST array.
In both cases, the microarray profiles show a significant bias for authentic neuronal transcripts as only 55% of all genes with expression patterns listed in WormBase are neuronal (Fig. 4) [See Additional file 4].
Their expression patterns are listed in Table 4.
Next, we analyzed the upstream sequences of the Calcium Channels query genes that were excluded from the Animal hit list based on their expression patterns.
EBSeq simultaneously assesses DE between multiple conditions by assigning a posterior probability to each possible expression pattern in an enumerated list of all possible expression patterns, given a set of conditions.
Selected contigs are listed in Table 5 and their expression patterns are shown in Supplementary Fig. S3b.
As shown in Table 2, columns "1", "2", "3", and "4" list the values of these four features for each miRNA; column "co-expressions" lists the correlation coefficients of the miRNA and host gene expression profiles; column "ER" lists the co-expression patterns of miRNA and host gene identified by biological experiments, in which "+" represents high co-expression and "−" represents low co-expression.
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