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Each line on the list is then linked to the corresponding target genes, descriptions for the TFBS and functional gene sets and the microarray conditions under which the target genes exhibit significant changes in expression.
Highly variable microarray experimental conditions and the use of different microarray platforms cause poor reproducibility of microarray measurements within and between laboratories [7] [11].
The Arabidopsis gene networks were previously reconstructed from global microarray conditions based on GGM [ 29] and co-expression analysis [ 32].
In other words, expression changes in the overlapping genes should be pronounced compared to the two individual sets [ 9]. (C) Number of conditions: Only TNs that satisfy the above two criteria (A) and (B) across k (default number =10) or more microarray conditions are regarded as reliable transcription patterns.
As in the case of the TF query, each line is linked to detailed information on the target genes, TFBS sets and the queried gene set as well as the corresponding microarray conditions.
All microarray conditions were collected in biological triplicates.
The conditions are described in Additional file 3. Additional file 3: Microarray conditions.
The 'number of conditions' leads to a table of the corresponding test/control microarray conditions.
Many known target genes as well as corresponding microarray conditions were identified.
Differentially expressed miRNA (DEmiR) was also tested using limma-like microarray conditions.
(C) Such changes should be observed across many microarray conditions (e.g. ten or more).
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