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Microarray chip information (from Affymetrix), raw data and results are stored in SoyXpress, and each probe is linked to the sequence information and meta-data.
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In this study, we present a novel methodology for unraveling transcriptional regulatory networks by integrated analysis of microarray, ChIP-chip data and TF motif information.
We further filtered by the presence of the predicted target gene on the microarray chip used in the experiment, information available at GEO datasets.
Thus, the SSH technology will have more utility in a system where genome sequence information and microarray chip are not available for transcript profiling.
For example, the relative expression levels of all the genes on a microarray chip translated into thousands of pieces of information.
The probe information for the Agilent microarray chip is based only on EST and cDNA sequences and thus is very limited.
The designed probes allow the production of quantitative information for Alexandrium species for the microarray chip.
We observed that the number of dmCpG sites for a gene was not dependent on the total number of CpG sites present on the microarray chip for the same gene (Pearson's correlation = 0.55, and Fig. S1, Supporting Information).
However, although much valuable information has been obtained in rice by microarray analysis using the Agilent 44 K microarray chip [ 23- 27], it remains possible that probes coding for some unidentified mRNAs and non-coding RNAs may not have been included in this chip.
We previously used a similar assay for the analysis of the Anopheles gambiæ salivary transcriptome [ 12] and obtained results overlapping very well with the information independently obtained by Marinotti et al. [ 13] using the Affymetrix microarray chip.
This database contains microarray data of 40 different experimental conditions obtained through microarray analysis using the same custom microarray chip as described in this manuscript.
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